├── .gitignore ├── Makefile ├── README.Rmd ├── README.md ├── Rmarkdown ├── header.tex ├── overview.png ├── references.bib ├── supplementary_file.Rmd └── supplementary_file.pdf ├── data ├── Arabidopsis_leaf_microbiome │ ├── BGCs_heatmap.csv │ ├── Interaction_link_tab.csv │ ├── Interaction_weight.csv │ ├── all_stain_taxonomy.csv │ └── stain_tippoint.csv ├── HMP_tree │ ├── barplot_attr.csv │ ├── hmptree.nwk │ ├── ringheatmap_attr.csv │ └── tippoint_attr.csv ├── Methanotroph │ ├── Methanotroph_rpS3_Modified_Alignment_RAxML │ └── metadata.csv ├── PhyloPhlAn │ ├── barplot_attr.csv │ ├── ppal_tol.nwk │ ├── ringpoint_attr.csv │ └── tippoint_attr.csv ├── VertebrateGutMicrobiomes │ ├── annotated_host_tree.tre │ ├── data_clade_class.csv │ ├── data_diet_bar.csv │ ├── data_flight_bar.csv │ ├── data_phylopic_uid.csv │ ├── ggtree_run.R │ └── mantel.jaccard.pearson.csv └── kegg │ ├── barplot_attr.csv │ ├── firstring_attr.csv │ ├── kegg.nwk │ ├── secondring_attr.csv │ └── tippoint_attr.csv ├── rawdata ├── Arabidopsis_leaf_microbiome │ └── EMS87355-supplement-Supplementary_Tables.xlsx ├── HMP_tree │ ├── annot.txt │ └── hmptree.xml ├── Methanotroph │ └── Methanotroph_rpS3_Metadata.csv ├── PhyloPhlAn │ ├── annot.txt │ └── ppa_tol.xml └── kegg │ ├── annot.txt │ └── kegg.xml └── scripts └── create_tree_and_dataframe.R /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | Rmarkdown/*.log 3 | Rmarkdown/Figures* 4 | Rmarkdown/Script*.R 5 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | # Makefile 2 | 3 | rd: 4 | Rscript -e 'rmarkdown::render("README.Rmd")' 5 | 6 | create_data: 7 | cd scripts;\ 8 | Rscript create_tree_and_dataframe.R 9 | 10 | supple: 11 | cd Rmarkdown;\ 12 | Rscript -e 'rmarkdown::render("supplementary_file.Rmd")';\ 13 | 14 | clean: 15 | rm Rmarkdown/supplementary_file.log 16 | 17 | update: 18 | git fetch origin master:utemp 19 | git merge utemp 20 | 21 | -------------------------------------------------------------------------------- /README.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: 3 | md_document: 4 | variant: gfm 5 | html_preview: false 6 | --- 7 | 8 | 9 | 10 | # ggtreeExtra: Compact visualization of richly annotated phylogenetic data 11 | 12 | If you use this work in published research, please cite: 13 | 14 | __S Xu__, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang^\*^, X Bo^\*^ and __G Yu__^\*. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. __*Molecular Biology and Evolution*__. 2021, 38(9):4039-4042. doi: [10.1093/molbev/msab166](https://doi.org/10.1093/molbev/msab166). 15 | 16 | 17 | This repo contains source code and data to produce Supplementary Material of the above paper. 18 | 19 | + rawdata: contains `HMP_tree`, `kegg` and `PhyloPhlAn`, downloaded from the examples of [GraPhlAn](https://github.com/biobakery/graphlan/tree/master/examples), and the `Methanotroph`, downloaded from the [repo](https://github.com/TheWrightonLab/Methanotroph_rpS3Analyses_SmithWrighton2018). 20 | + scripts: contains the script to produce the dataset of `data` using the data set of `rawdata`. 21 | + data: contains all the data sets that used to generate figures in Supplemental file. 22 | + Rmarkdown: contains the source code to produce Supplementary File. 23 | 24 | 25 | ## Dependencies and locations 26 | 27 | 28 | 29 | 30 | + R (>= 4.0.3) should be installed and located in the user's PATH, and the following packages should be installed. 31 | - `ggtreeExtra` : `BiocManager::install("ggtreeExtra")` 32 | - `ggtree` : `BiocManager::install("ggtree")` 33 | - `treeio` : `BiocManager::install("treeio")` 34 | - `tidytree` : `install.packages("tidytree")` 35 | - `ggplot2` : `install.packages("ggplot2")` 36 | - `kableExtra` : `install.packages("kableExtra")` 37 | - `bookdown` : `install.package("bookdown")` 38 | - `MicrobiotaProcess` : `BiocManager::install("MicrobiotaProcess")` 39 | - `ggstar` : `install.packages("ggstar")` 40 | - `Cairo` : `install.packages("Cairo")` 41 | - `aplot` : `install.packages("aplot")` 42 | - `patchwork` : `install.packages("patchwork")` 43 | - `ggnewscale` : `install.packages("ggnewscale")` 44 | - `knitr` : `install.packages("knitr")` 45 | - `ggpp` : `install.packages("ggpp")` 46 | - [`ggpattern`](https://github.com/coolbutuseless/ggpattern) : `remotes::install_github("coolbutuseless/ggpattern")` 47 | - `tibble` : `install.packages("tibble")` 48 | - `tidyr` : `install.packages("tidyr")` 49 | - `dplyr` : `install.packages("dplyr")` 50 | - `ggimage` : `install.packages("ggimage")` 51 | - `ggridges` : `install.packages("ggridges")` 52 | 53 | ```{r, message=FALSE, echo=FALSE, setup} 54 | library(ggtreeExtra) 55 | library(ggstar) 56 | library(ggplot2) 57 | library(ggtree) 58 | library(treeio) 59 | library(tidytree) 60 | library(ggnewscale) 61 | library(MicrobiotaProcess) 62 | library(aplot) 63 | library(kableExtra) 64 | library(Cairo) 65 | library(patchwork) 66 | library(knitr) 67 | library(ggpattern) 68 | library(ggpp) 69 | library(ggridges) 70 | library(tidyr) 71 | library(dplyr) 72 | library(tibble) 73 | library(ggimage) 74 | ``` 75 | 76 | To compile the Rmarkdown/[supplemental_file.pdf](Rmarkdown/supplementary_file.pdf), please run the following command on terminal. 77 | 78 | 81 | 82 | ```bash 83 | Rscript -e 'rmarkdown::render("./Rmarkdown/supplementary_file.Rmd")' 84 | ``` 85 | 86 | Or run the following command in R. 87 | 88 | ```r 89 | rmarkdown::render("./Rmarkdown/supplementary_file.Rmd") 90 | ``` 91 | 92 | Here is the output of `sessionInfo()` of the system on which [the Supplemental file](Rmarkdown/supplementary_file.pdf) was compiled: 93 | 94 | ```{r, echo=FALSE} 95 | sessionInfo() 96 | ``` 97 | 98 | ## Docker image 99 | 100 | We also provided a [docker image](https://hub.docker.com/r/xushuangbin/ggtreeextraarticleenv) to help users to build the computing environment. You can pull and run it according to the following commands. 101 | 102 | - Install Docker (https://www.docker.com/) 103 | - `sudo apt-get install docker.io` (Ubuntu) 104 | - Pull the Docker image from Docker Hub: 105 | - `docker pull xushuangbin/ggtreeextraarticleenv:latest` 106 | - or 107 | - `sudo pull xushuangbin/ggtreeextraarticleenv:latest` 108 | - Run the image: 109 | - `docker run -e PASSWORD=yourpassword -p 8787:8787 xushuangbin/ggtreeextraarticleenv` 110 | - or 111 | - `sudo docker run -e PASSWORD=yourpassword -p 8787:8787 xushuangbin/ggtreeextraarticleenv` 112 | - Log in to RStudio at [http://localhost:8787](http://localhost:8787) using username `rstudio` and password `yourpassword`. For Windows users, you also need to provide your IP address, you can find it using `docker-machine ip default`. 113 | + Inside the RStudio, run: 114 | `browseVignettes(package = "ggtreeExtraArticleEnv")` 115 | - You can click one of the links: "PDF", "source", "R code" 116 | - In case of `The requested page was not found` error, try add 'help/' in front of the hostname in the URL (this is a known bug): 117 | http://localhost:8787/help/library/ggtreeExtraArticleEnv/doc/supplementary_file.pdf 118 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | 3 | # ggtreeExtra: Compact visualization of richly annotated phylogenetic data 4 | 5 | If you use this work in published research, please cite: 6 | 7 | **S Xu**, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L 8 | Zhan, T Wu, E Hu, Y Jiang^\*, X Bo^\* and **G 9 | Yu**^\*. ggtreeExtra: Compact visualization of richly 10 | annotated phylogenetic data. ***Molecular Biology and Evolution***. 11 | 2021, 38(9):4039-4042. doi: 12 | [10.1093/molbev/msab166](https://doi.org/10.1093/molbev/msab166). 13 | 14 | This repo contains source code and data to produce 15 | Supplementary Material of the above paper. 16 | 17 | - rawdata: contains `HMP_tree`, `kegg` and `PhyloPhlAn`, downloaded 18 | from the examples of 19 | [GraPhlAn](https://github.com/biobakery/graphlan/tree/master/examples), 20 | and the `Methanotroph`, downloaded from the 21 | [repo](https://github.com/TheWrightonLab/Methanotroph_rpS3Analyses_SmithWrighton2018). 22 | - scripts: contains the script to produce the dataset of `data` using 23 | the data set of `rawdata`. 24 | - data: contains all the data sets that used to generate figures in 25 | Supplemental file. 26 | - Rmarkdown: contains the source code to produce Supplementary File. 27 | 28 | ## Dependencies and locations 29 | 30 | 31 | 32 | 33 | 34 | - R (\>= 4.0.3) should be installed and located in the user’s PATH, 35 | and the following packages should be installed. 36 | - `ggtreeExtra` : `BiocManager::install("ggtreeExtra")` 37 | - `ggtree` : `BiocManager::install("ggtree")` 38 | - `treeio` : `BiocManager::install("treeio")` 39 | - `tidytree` : `install.packages("tidytree")` 40 | - `ggplot2` : `install.packages("ggplot2")` 41 | - `kableExtra` : `install.packages("kableExtra")` 42 | - `bookdown` : `install.package("bookdown")` 43 | - `MicrobiotaProcess` : 44 | `BiocManager::install("MicrobiotaProcess")` 45 | - `ggstar` : `install.packages("ggstar")` 46 | - `Cairo` : `install.packages("Cairo")` 47 | - `aplot` : `install.packages("aplot")` 48 | - `patchwork` : `install.packages("patchwork")` 49 | - `ggnewscale` : `install.packages("ggnewscale")` 50 | - `knitr` : `install.packages("knitr")` 51 | - `ggpp` : `install.packages("ggpp")` 52 | - [`ggpattern`](https://github.com/coolbutuseless/ggpattern) : 53 | `remotes::install_github("coolbutuseless/ggpattern")` 54 | - `tibble` : `install.packages("tibble")` 55 | - `tidyr` : `install.packages("tidyr")` 56 | - `dplyr` : `install.packages("dplyr")` 57 | - `ggimage` : `install.packages("ggimage")` 58 | - `ggridges` : `install.packages("ggridges")` 59 | 60 | To compile the 61 | Rmarkdown/[supplemental\_file.pdf](Rmarkdown/supplementary_file.pdf), 62 | please run the following command on terminal. 63 | 64 | 67 | 68 | ``` bash 69 | Rscript -e 'rmarkdown::render("./Rmarkdown/supplementary_file.Rmd")' 70 | ``` 71 | 72 | Or run the following command in R. 73 | 74 | ``` r 75 | rmarkdown::render("./Rmarkdown/supplementary_file.Rmd") 76 | ``` 77 | 78 | Here is the output of `sessionInfo()` of the system on which [the 79 | Supplemental file](Rmarkdown/supplementary_file.pdf) was compiled: 80 | 81 | ## R version 4.1.0 (2021-05-18) 82 | ## Platform: x86_64-pc-linux-gnu (64-bit) 83 | ## Running under: Ubuntu 18.04.4 LTS 84 | ## 85 | ## Matrix products: default 86 | ## BLAS: /mnt/d/UbuntuApps/R/4.1.0/lib/R/lib/libRblas.so 87 | ## LAPACK: /mnt/d/UbuntuApps/R/4.1.0/lib/R/lib/libRlapack.so 88 | ## 89 | ## locale: 90 | ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 91 | ## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 92 | ## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 93 | ## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C 94 | ## [9] LC_ADDRESS=C LC_TELEPHONE=C 95 | ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C 96 | ## 97 | ## attached base packages: 98 | ## [1] stats graphics grDevices utils datasets methods base 99 | ## 100 | ## other attached packages: 101 | ## [1] ggimage_0.2.9 tibble_3.1.2 102 | ## [3] dplyr_1.0.7 tidyr_1.1.3 103 | ## [5] ggridges_0.5.3 ggpp_0.4.0 104 | ## [7] ggpattern_0.1.3 knitr_1.33 105 | ## [9] patchwork_1.1.1 Cairo_1.5-12.2 106 | ## [11] kableExtra_1.3.4 aplot_0.0.6 107 | ## [13] MicrobiotaProcess_1.5.3.992 ggnewscale_0.4.5 108 | ## [15] tidytree_0.3.4.991 treeio_1.17.2 109 | ## [17] ggtree_3.1.3.991 ggplot2_3.3.5 110 | ## [19] ggstar_1.0.2.991 ggtreeExtra_1.3.3 111 | ## 112 | ## loaded via a namespace (and not attached): 113 | ## [1] TH.data_1.0-10 colorspace_2.0-2 114 | ## [3] ggsignif_0.6.3 class_7.3-19 115 | ## [5] ellipsis_0.3.2 modeltools_0.2-23 116 | ## [7] XVector_0.32.0 GenomicRanges_1.44.0 117 | ## [9] proxy_0.4-26 rstudioapi_0.13 118 | ## [11] ggrepel_0.9.1 fansi_0.5.0 119 | ## [13] mvtnorm_1.1-2 coin_1.4-1 120 | ## [15] xml2_1.3.2 codetools_0.2-18 121 | ## [17] splines_4.1.0 libcoin_1.0-8 122 | ## [19] polyclip_1.10-0 ade4_1.7-17 123 | ## [21] jsonlite_1.7.2 phyloseq_1.36.0 124 | ## [23] cluster_2.1.2 png_0.1-7 125 | ## [25] compiler_4.1.0 httr_1.4.2 126 | ## [27] assertthat_0.2.1 Matrix_1.3-4 127 | ## [29] lazyeval_0.2.2 htmltools_0.5.1.1 128 | ## [31] tools_4.1.0 igraph_1.2.6 129 | ## [33] gtable_0.3.0 glue_1.4.2 130 | ## [35] GenomeInfoDbData_1.2.6 reshape2_1.4.4 131 | ## [37] Rcpp_1.0.6 Biobase_2.52.0 132 | ## [39] vctrs_0.3.8 Biostrings_2.60.1 133 | ## [41] rhdf5filters_1.4.0 multtest_2.48.0 134 | ## [43] ape_5.5 svglite_2.0.0 135 | ## [45] nlme_3.1-152 iterators_1.0.13 136 | ## [47] xfun_0.24 stringr_1.4.0 137 | ## [49] rvest_1.0.0 lifecycle_1.0.0 138 | ## [51] zlibbioc_1.38.0 MASS_7.3-54 139 | ## [53] zoo_1.8-9 scales_1.1.1 140 | ## [55] MatrixGenerics_1.4.0 parallel_4.1.0 141 | ## [57] SummarizedExperiment_1.22.0 biomformat_1.20.0 142 | ## [59] sandwich_3.0-1 rhdf5_2.36.0 143 | ## [61] yaml_2.2.1 gridGeometry_0.2-0 144 | ## [63] gridExtra_2.3 ggfun_0.0.3 145 | ## [65] yulab.utils_0.0.3 stringi_1.6.2 146 | ## [67] S4Vectors_0.30.0 foreach_1.5.1 147 | ## [69] e1071_1.7-7 permute_0.9-5 148 | ## [71] BiocGenerics_0.38.0 GenomeInfoDb_1.28.0 149 | ## [73] rlang_0.4.11 pkgconfig_2.0.3 150 | ## [75] systemfonts_1.0.2 matrixStats_0.59.0 151 | ## [77] bitops_1.0-7 evaluate_0.14 152 | ## [79] lattice_0.20-44 sf_1.0-0 153 | ## [81] purrr_0.3.4 Rhdf5lib_1.14.1 154 | ## [83] tidyselect_1.1.1 plyr_1.8.6 155 | ## [85] magrittr_2.0.1 R6_2.5.0 156 | ## [87] IRanges_2.26.0 magick_2.7.2 157 | ## [89] generics_0.1.0 multcomp_1.4-17 158 | ## [91] DelayedArray_0.18.0 DBI_1.1.1 159 | ## [93] pillar_1.6.1 withr_2.4.2 160 | ## [95] mgcv_1.8-36 units_0.7-2 161 | ## [97] survival_3.2-11 RCurl_1.98-1.3 162 | ## [99] crayon_1.4.1 KernSmooth_2.23-20 163 | ## [101] utf8_1.2.1 rmarkdown_2.9.7 164 | ## [103] grid_4.1.0 data.table_1.14.0 165 | ## [105] vegan_2.5-7 classInt_0.4-3 166 | ## [107] digest_0.6.27 webshot_0.5.2 167 | ## [109] gridGraphics_0.5-1 stats4_4.1.0 168 | ## [111] munsell_0.5.0 ggplotify_0.0.9 169 | ## [113] viridisLite_0.4.0 170 | 171 | ## Docker image 172 | 173 | We also provided a [docker 174 | image](https://hub.docker.com/r/xushuangbin/ggtreeextraarticleenv) to 175 | help users to build the computing environment. You can pull and run it 176 | according to the following commands. 177 | 178 | - Install Docker () 179 | - `sudo apt-get install docker.io` (Ubuntu) 180 | - Pull the Docker image from Docker Hub: 181 | - `docker pull xushuangbin/ggtreeextraarticleenv:latest` 182 | - or 183 | - `sudo pull xushuangbin/ggtreeextraarticleenv:latest` 184 | - Run the image: 185 | - `docker run -e PASSWORD=yourpassword -p 8787:8787 186 | xushuangbin/ggtreeextraarticleenv` 187 | - or 188 | - `sudo docker run -e PASSWORD=yourpassword -p 8787:8787 189 | xushuangbin/ggtreeextraarticleenv` 190 | - Log in to RStudio at using username 191 | `rstudio` and password `yourpassword`. For Windows users, you also 192 | need to provide your IP address, you can find it using 193 | `docker-machine ip default`. 194 | - Inside the RStudio, run: `browseVignettes(package = 195 | "ggtreeExtraArticleEnv")` 196 | - You can click one of the links: “PDF”, “source”, “R code” 197 | - In case of `The requested page was not found` error, try add ‘help/’ 198 | in front of the hostname in the URL (this is a known bug): 199 | 200 | -------------------------------------------------------------------------------- /Rmarkdown/header.tex: -------------------------------------------------------------------------------- 1 | \usepackage{booktabs} 2 | \usepackage{longtable} 3 | \usepackage{array} 4 | \usepackage{multirow} 5 | \usepackage{wrapfig} 6 | \usepackage{float} 7 | \usepackage{colortbl} 8 | \usepackage{pdflscape} 9 | \usepackage{tabu} 10 | \usepackage{threeparttable} 11 | \usepackage[normalem]{ulem} 12 | -------------------------------------------------------------------------------- /Rmarkdown/overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/plotting-tree-with-data-using-ggtreeExtra/4e089aa5caea12c3e6110e07dbb257c7b6e25214/Rmarkdown/overview.png -------------------------------------------------------------------------------- /Rmarkdown/supplementary_file.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/plotting-tree-with-data-using-ggtreeExtra/4e089aa5caea12c3e6110e07dbb257c7b6e25214/Rmarkdown/supplementary_file.pdf -------------------------------------------------------------------------------- /data/Arabidopsis_leaf_microbiome/Interaction_link_tab.csv: -------------------------------------------------------------------------------- 1 | Inhibitor,Sensitive,Interaction 2 | s__Leaf11,s__Leaf294,weak 3 | s__Leaf11,s__Leaf326,strong 4 | s__Leaf11,s__Leaf341,weak 5 | s__Leaf11,s__Leaf344,weak 6 | 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s__Leaf154,s__Leaf380,strong 131 | s__Leaf154,s__Leaf408,weak 132 | s__Leaf154,s__Leaf446,weak 133 | s__Leaf154,s__Leaf8,weak 134 | s__Leaf154,s__Leaf82,weak 135 | s__Leaf154,s__Leaf84,weak 136 | s__Leaf154,s__Leaf89,weak 137 | s__Leaf154,s__Leaf72,weak 138 | s__Leaf16,s__Leaf280,weak 139 | s__Leaf16,s__Leaf92,weak 140 | s__Leaf161,s__Leaf4,weak 141 | s__Leaf167,s__Leaf113,weak 142 | s__Leaf167,s__Leaf189,weak 143 | s__Leaf167,s__Leaf155,weak 144 | s__Leaf170,s__Leaf189,weak 145 | s__Leaf176,s__Leaf113,weak 146 | s__Leaf176,s__Leaf92,weak 147 | s__Leaf177,s__Leaf208,weak 148 | s__Leaf177,s__Leaf325,weak 149 | s__Leaf177,s__Leaf341,weak 150 | s__Leaf177,s__Leaf361,weak 151 | s__Leaf177,s__Leaf394,strong 152 | s__Leaf177,s__Leaf404,weak 153 | s__Leaf177,s__Leaf427,weak 154 | s__Leaf177,s__Leaf436,weak 155 | s__Leaf182,s__Leaf1,weak 156 | s__Leaf182,s__Leaf10,weak 157 | s__Leaf182,s__Leaf100,weak 158 | s__Leaf182,s__Leaf102,weak 159 | s__Leaf182,s__Leaf106,weak 160 | s__Leaf182,s__Leaf11,strong 161 | s__Leaf182,s__Leaf111,weak 162 | s__Leaf182,s__Leaf112,weak 163 | s__Leaf182,s__Leaf113,weak 164 | s__Leaf182,s__Leaf117,weak 165 | s__Leaf182,s__Leaf122,weak 166 | s__Leaf182,s__Leaf123,weak 167 | s__Leaf182,s__Leaf125,weak 168 | s__Leaf182,s__Leaf130,weak 169 | s__Leaf182,s__Leaf16,strong 170 | s__Leaf182,s__Leaf160,weak 171 | s__Leaf182,s__Leaf17,strong 172 | s__Leaf182,s__Leaf172,weak 173 | s__Leaf182,s__Leaf177,weak 174 | s__Leaf182,s__Leaf183,weak 175 | s__Leaf182,s__Leaf185,weak 176 | s__Leaf182,s__Leaf186,weak 177 | s__Leaf182,s__Leaf189,weak 178 | s__Leaf182,s__Leaf191,weak 179 | s__Leaf182,s__Leaf198,weak 180 | s__Leaf182,s__Leaf2,strong 181 | s__Leaf182,s__Leaf20,weak 182 | s__Leaf182,s__Leaf205,weak 183 | s__Leaf182,s__Leaf208,weak 184 | s__Leaf182,s__Leaf21,weak 185 | s__Leaf182,s__Leaf22,strong 186 | s__Leaf182,s__Leaf220,strong 187 | s__Leaf182,s__Leaf225,weak 188 | s__Leaf182,s__Leaf226,weak 189 | s__Leaf182,s__Leaf23,weak 190 | s__Leaf182,s__Leaf230,weak 191 | s__Leaf182,s__Leaf234,strong 192 | s__Leaf182,s__Leaf24,weak 193 | s__Leaf182,s__Leaf242,strong 194 | s__Leaf182,s__Leaf244,weak 195 | s__Leaf182,s__Leaf248,weak 196 | s__Leaf182,s__Leaf25,strong 197 | s__Leaf182,s__Leaf258,weak 198 | s__Leaf182,s__Leaf263,weak 199 | s__Leaf182,s__Leaf265,weak 200 | s__Leaf182,s__Leaf267,weak 201 | s__Leaf182,s__Leaf28,strong 202 | s__Leaf182,s__Leaf283,weak 203 | s__Leaf182,s__Leaf285,weak 204 | s__Leaf182,s__Leaf289,weak 205 | s__Leaf182,s__Leaf29,strong 206 | s__Leaf182,s__Leaf291,strong 207 | s__Leaf182,s__Leaf3,strong 208 | s__Leaf182,s__Leaf30,strong 209 | s__Leaf182,s__Leaf304,strong 210 | s__Leaf182,s__Leaf307,weak 211 | s__Leaf182,s__Leaf32,strong 212 | s__Leaf182,s__Leaf326,weak 213 | s__Leaf182,s__Leaf33,strong 214 | s__Leaf182,s__Leaf335,weak 215 | s__Leaf182,s__Leaf339,weak 216 | s__Leaf182,s__Leaf34,weak 217 | s__Leaf182,s__Leaf343,weak 218 | s__Leaf182,s__Leaf347,weak 219 | s__Leaf182,s__Leaf350,weak 220 | s__Leaf182,s__Leaf351,weak 221 | s__Leaf182,s__Leaf354,weak 222 | s__Leaf182,s__Leaf357,strong 223 | s__Leaf182,s__Leaf363,weak 224 | s__Leaf182,s__Leaf37,strong 225 | s__Leaf182,s__Leaf374,weak 226 | s__Leaf182,s__Leaf38,strong 227 | s__Leaf182,s__Leaf380,weak 228 | s__Leaf182,s__Leaf386,weak 229 | s__Leaf182,s__Leaf391,weak 230 | s__Leaf182,s__Leaf395,weak 231 | s__Leaf182,s__Leaf396,weak 232 | s__Leaf182,s__Leaf399,weak 233 | s__Leaf182,s__Leaf400,strong 234 | s__Leaf182,s__Leaf401,strong 235 | s__Leaf182,s__Leaf407,weak 236 | s__Leaf182,s__Leaf41,strong 237 | s__Leaf182,s__Leaf42,strong 238 | s__Leaf182,s__Leaf420,weak 239 | s__Leaf182,s__Leaf427,weak 240 | s__Leaf182,s__Leaf44,strong 241 | s__Leaf182,s__Leaf443,weak 242 | s__Leaf182,s__Leaf446,weak 243 | s__Leaf182,s__Leaf453,strong 244 | s__Leaf182,s__Leaf456,weak 245 | s__Leaf182,s__Leaf459,weak 246 | s__Leaf182,s__Leaf460,weak 247 | s__Leaf182,s__Leaf466,weak 248 | s__Leaf182,s__Leaf49,weak 249 | s__Leaf182,s__Leaf5,strong 250 | s__Leaf182,s__Leaf62,strong 251 | s__Leaf182,s__Leaf64,strong 252 | s__Leaf182,s__Leaf67,strong 253 | s__Leaf182,s__Leaf7,weak 254 | s__Leaf182,s__Leaf8,strong 255 | s__Leaf182,s__Leaf84,weak 256 | s__Leaf182,s__Leaf85,weak 257 | s__Leaf182,s__Leaf86,weak 258 | s__Leaf182,s__Leaf87,weak 259 | s__Leaf182,s__Leaf89,weak 260 | s__Leaf182,s__Leaf9,strong 261 | s__Leaf182,s__Leaf90,weak 262 | s__Leaf182,s__Leaf91,weak 263 | s__Leaf182,s__Leaf93,weak 264 | s__Leaf182,s__Leaf99,weak 265 | s__Leaf182,s__Leaf72,weak 266 | s__Leaf187,s__Leaf189,weak 267 | s__Leaf187,s__Leaf226,weak 268 | s__Leaf187,s__Leaf28,weak 269 | s__Leaf187,s__Leaf29,weak 270 | s__Leaf187,s__Leaf30,weak 271 | s__Leaf187,s__Leaf32,weak 272 | s__Leaf187,s__Leaf33,weak 273 | s__Leaf187,s__Leaf339,weak 274 | s__Leaf187,s__Leaf34,weak 275 | s__Leaf187,s__Leaf363,weak 276 | s__Leaf187,s__Leaf38,weak 277 | s__Leaf191,s__Leaf38,weak 278 | s__Leaf194,s__Leaf189,weak 279 | s__Leaf194,s__Leaf314,weak 280 | s__Leaf194,s__Leaf416,weak 281 | s__Leaf196,s__Leaf1,weak 282 | s__Leaf196,s__Leaf17,strong 283 | s__Leaf196,s__Leaf189,weak 284 | s__Leaf196,s__Leaf208,weak 285 | s__Leaf196,s__Leaf23,weak 286 | s__Leaf196,s__Leaf28,strong 287 | s__Leaf196,s__Leaf30,weak 288 | s__Leaf196,s__Leaf314,weak 289 | s__Leaf196,s__Leaf33,strong 290 | s__Leaf196,s__Leaf34,weak 291 | s__Leaf196,s__Leaf363,weak 292 | s__Leaf196,s__Leaf37,weak 293 | s__Leaf196,s__Leaf38,weak 294 | s__Leaf196,s__Leaf4,weak 295 | s__Leaf196,s__Leaf443,weak 296 | s__Leaf196,s__Leaf9,weak 297 | s__Leaf196,s__Leaf72,weak 298 | s__Leaf2,s__Leaf180,weak 299 | s__Leaf2,s__Leaf182,weak 300 | s__Leaf2,s__Leaf186,weak 301 | s__Leaf2,s__Leaf205,strong 302 | s__Leaf2,s__Leaf208,weak 303 | s__Leaf2,s__Leaf226,weak 304 | s__Leaf2,s__Leaf234,weak 305 | s__Leaf2,s__Leaf242,strong 306 | s__Leaf2,s__Leaf258,weak 307 | s__Leaf2,s__Leaf289,weak 308 | s__Leaf2,s__Leaf291,weak 309 | s__Leaf2,s__Leaf304,weak 310 | s__Leaf2,s__Leaf307,weak 311 | s__Leaf2,s__Leaf326,weak 312 | s__Leaf2,s__Leaf335,weak 313 | s__Leaf2,s__Leaf341,weak 314 | s__Leaf2,s__Leaf347,weak 315 | s__Leaf2,s__Leaf350,weak 316 | s__Leaf2,s__Leaf354,weak 317 | s__Leaf2,s__Leaf369,weak 318 | s__Leaf2,s__Leaf374,weak 319 | s__Leaf2,s__Leaf394,strong 320 | s__Leaf2,s__Leaf395,weak 321 | s__Leaf2,s__Leaf400,weak 322 | s__Leaf2,s__Leaf401,weak 323 | s__Leaf2,s__Leaf404,weak 324 | s__Leaf2,s__Leaf407,weak 325 | s__Leaf2,s__Leaf416,weak 326 | s__Leaf2,s__Leaf436,weak 327 | s__Leaf2,s__Leaf443,strong 328 | s__Leaf2,s__Leaf459,strong 329 | s__Leaf201,s__Leaf17,weak 330 | s__Leaf201,s__Leaf446,weak 331 | s__Leaf201,s__Leaf72,weak 332 | s__Leaf202,s__Leaf111,weak 333 | s__Leaf202,s__Leaf113,weak 334 | s__Leaf202,s__Leaf17,weak 335 | s__Leaf202,s__Leaf30,weak 336 | s__Leaf202,s__Leaf33,strong 337 | s__Leaf202,s__Leaf155,weak 338 | s__Leaf203,s__Leaf111,weak 339 | s__Leaf203,s__Leaf113,weak 340 | s__Leaf21,s__Leaf9,weak 341 | s__Leaf23,s__Leaf351,weak 342 | s__Leaf245,s__Leaf285,strong 343 | s__Leaf245,s__Leaf307,strong 344 | s__Leaf245,s__Leaf374,strong 345 | s__Leaf245,s__Leaf446,weak 346 | s__Leaf250,s__Leaf113,weak 347 | s__Leaf254,s__Leaf401,weak 348 | s__Leaf254,s__Leaf443,weak 349 | s__Leaf262,s__Leaf394,weak 350 | s__Leaf264,s__Leaf335,weak 351 | s__Leaf272,s__Leaf285,weak 352 | s__Leaf272,s__Leaf30,weak 353 | s__Leaf272,s__Leaf307,weak 354 | s__Leaf272,s__Leaf374,weak 355 | s__Leaf272,s__Leaf38,weak 356 | s__Leaf272,s__Leaf446,weak 357 | s__Leaf28,s__Leaf132,weak 358 | s__Leaf280,s__Leaf151,weak 359 | s__Leaf285,s__Leaf208,weak 360 | s__Leaf285,s__Leaf38,weak 361 | s__Leaf285,s__Leaf5,weak 362 | s__Leaf289,s__Leaf285,weak 363 | s__Leaf289,s__Leaf446,weak 364 | s__Leaf291,s__Leaf285,weak 365 | s__Leaf291,s__Leaf446,weak 366 | s__Leaf30,s__Leaf294,weak 367 | s__Leaf30,s__Leaf326,strong 368 | s__Leaf30,s__Leaf357,strong 369 | s__Leaf30,s__Leaf394,strong 370 | s__Leaf30,s__Leaf400,weak 371 | s__Leaf30,s__Leaf401,strong 372 | 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432 | s__Leaf408,s__Leaf401,strong 433 | s__Leaf408,s__Leaf404,strong 434 | s__Leaf408,s__Leaf407,strong 435 | s__Leaf408,s__Leaf412,weak 436 | s__Leaf408,s__Leaf427,weak 437 | s__Leaf408,s__Leaf443,strong 438 | s__Leaf434,s__Leaf1,strong 439 | s__Leaf434,s__Leaf10,weak 440 | s__Leaf434,s__Leaf111,weak 441 | s__Leaf434,s__Leaf113,weak 442 | s__Leaf434,s__Leaf117,weak 443 | s__Leaf434,s__Leaf126,weak 444 | s__Leaf434,s__Leaf131,weak 445 | s__Leaf434,s__Leaf148,weak 446 | s__Leaf434,s__Leaf151,weak 447 | s__Leaf434,s__Leaf16,weak 448 | s__Leaf434,s__Leaf17,strong 449 | s__Leaf434,s__Leaf179,weak 450 | s__Leaf434,s__Leaf186,strong 451 | s__Leaf434,s__Leaf198,weak 452 | s__Leaf434,s__Leaf20,weak 453 | s__Leaf434,s__Leaf205,weak 454 | s__Leaf434,s__Leaf220,weak 455 | s__Leaf434,s__Leaf225,weak 456 | s__Leaf434,s__Leaf226,weak 457 | s__Leaf434,s__Leaf234,weak 458 | s__Leaf434,s__Leaf28,weak 459 | s__Leaf434,s__Leaf30,weak 460 | s__Leaf434,s__Leaf32,weak 461 | s__Leaf434,s__Leaf320,weak 462 | s__Leaf434,s__Leaf321,weak 463 | s__Leaf434,s__Leaf326,strong 464 | s__Leaf434,s__Leaf33,weak 465 | s__Leaf434,s__Leaf335,weak 466 | s__Leaf434,s__Leaf34,weak 467 | s__Leaf434,s__Leaf341,weak 468 | s__Leaf434,s__Leaf343,weak 469 | s__Leaf434,s__Leaf344,weak 470 | s__Leaf434,s__Leaf347,weak 471 | s__Leaf434,s__Leaf357,weak 472 | s__Leaf434,s__Leaf361,weak 473 | s__Leaf434,s__Leaf369,weak 474 | s__Leaf434,s__Leaf37,weak 475 | s__Leaf434,s__Leaf38,weak 476 | s__Leaf434,s__Leaf384,weak 477 | s__Leaf434,s__Leaf394,weak 478 | s__Leaf434,s__Leaf4,weak 479 | s__Leaf434,s__Leaf400,weak 480 | s__Leaf434,s__Leaf401,weak 481 | s__Leaf434,s__Leaf404,strong 482 | s__Leaf434,s__Leaf407,weak 483 | s__Leaf434,s__Leaf408,weak 484 | s__Leaf434,s__Leaf414,weak 485 | s__Leaf434,s__Leaf416,weak 486 | s__Leaf434,s__Leaf436,weak 487 | s__Leaf434,s__Leaf443,weak 488 | s__Leaf434,s__Leaf446,weak 489 | s__Leaf434,s__Leaf459,weak 490 | s__Leaf434,s__Leaf466,weak 491 | s__Leaf434,s__Leaf62,strong 492 | s__Leaf434,s__Leaf67,weak 493 | s__Leaf434,s__Leaf89,weak 494 | s__Leaf44,s__Leaf446,weak 495 | s__Leaf465,s__Leaf172,weak 496 | s__Leaf465,s__Leaf42,weak 497 | s__Leaf465,s__Leaf62,strong 498 | s__Leaf48,s__Leaf394,weak 499 | s__Leaf49,s__Leaf1,weak 500 | s__Leaf49,s__Leaf10,weak 501 | s__Leaf49,s__Leaf16,weak 502 | s__Leaf49,s__Leaf186,weak 503 | s__Leaf49,s__Leaf208,weak 504 | s__Leaf49,s__Leaf23,weak 505 | s__Leaf49,s__Leaf24,weak 506 | s__Leaf49,s__Leaf25,weak 507 | s__Leaf49,s__Leaf26,weak 508 | s__Leaf49,s__Leaf263,weak 509 | s__Leaf49,s__Leaf267,weak 510 | s__Leaf49,s__Leaf28,strong 511 | s__Leaf49,s__Leaf30,strong 512 | s__Leaf49,s__Leaf326,strong 513 | s__Leaf49,s__Leaf33,strong 514 | s__Leaf49,s__Leaf34,strong 515 | s__Leaf49,s__Leaf351,weak 516 | s__Leaf49,s__Leaf37,weak 517 | s__Leaf49,s__Leaf38,strong 518 | s__Leaf49,s__Leaf395,weak 519 | s__Leaf49,s__Leaf4,weak 520 | s__Leaf49,s__Leaf401,weak 521 | s__Leaf49,s__Leaf404,weak 522 | s__Leaf49,s__Leaf41,strong 523 | 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Weak,0 352 | s__Leaf225,Inhibitor Weak,0 353 | s__Leaf230,Inhibitor Weak,0 354 | s__Leaf258,Inhibitor Weak,0 355 | s__Leaf320,Inhibitor Weak,0 356 | s__Leaf325,Inhibitor Weak,0 357 | s__Leaf350,Inhibitor Weak,0 358 | s__Leaf354,Inhibitor Weak,0 359 | s__Leaf396,Inhibitor Weak,0 360 | s__Leaf414,Inhibitor Weak,0 361 | s__Leaf416,Inhibitor Weak,0 362 | s__Leaf87,Inhibitor Weak,0 363 | s__Leaf91,Inhibitor Weak,0 364 | s__Leaf99,Inhibitor Weak,0 365 | s__Leaf172,Inhibitor Weak,0 366 | s__Leaf185,Inhibitor Weak,0 367 | s__Leaf24,Inhibitor Weak,0 368 | s__Leaf263,Inhibitor Weak,0 369 | s__Leaf283,Inhibitor Weak,0 370 | s__Leaf299,Inhibitor Weak,0 371 | s__Leaf314,Inhibitor Weak,0 372 | s__Leaf361,Inhibitor Weak,0 373 | s__Leaf399,Inhibitor Weak,0 374 | s__Leaf412,Inhibitor Weak,0 375 | s__Leaf460,Inhibitor Weak,0 376 | s__Leaf7,Inhibitor Weak,0 377 | s__Leaf86,Inhibitor Weak,0 378 | s__Leaf108,Inhibitor Weak,0 379 | s__Leaf118,Inhibitor Weak,0 380 | s__Leaf119,Inhibitor Weak,0 381 | s__Leaf160,Inhibitor Weak,0 382 | s__Leaf179,Inhibitor Weak,0 383 | s__Leaf183,Inhibitor Weak,0 384 | s__Leaf231,Inhibitor Weak,0 385 | s__Leaf244,Inhibitor Weak,0 386 | s__Leaf248,Inhibitor Weak,0 387 | s__Leaf26,Inhibitor Weak,0 388 | s__Leaf265,Inhibitor Weak,0 389 | s__Leaf296,Inhibitor Weak,0 390 | s__Leaf321,Inhibitor Weak,0 391 | s__Leaf386,Inhibitor Weak,0 392 | s__Leaf391,Inhibitor Weak,0 393 | s__Leaf415,Inhibitor Weak,0 394 | s__Leaf85,Inhibitor Weak,0 395 | s__Leaf88,Inhibitor Weak,0 396 | s__Leaf182,Sensitive Strong,0 397 | s__Leaf98,Sensitive Strong,0 398 | s__Leaf434,Sensitive Strong,0 399 | s__Leaf58,Sensitive Strong,0 400 | s__Leaf15,Sensitive Strong,0 401 | s__Leaf49,Sensitive Strong,0 402 | s__Leaf2,Sensitive Strong,1 403 | s__Leaf408,Sensitive Strong,0 404 | s__Leaf75,Sensitive Strong,0 405 | s__Leaf82,Sensitive Strong,0 406 | s__Leaf196,Sensitive Strong,0 407 | s__Leaf154,Sensitive Strong,0 408 | s__Leaf11,Sensitive Strong,1 409 | s__Leaf126,Sensitive Strong,0 410 | s__Leaf130,Sensitive Strong,0 411 | s__Leaf187,Sensitive Strong,0 412 | s__Leaf30,Sensitive Strong,2 413 | s__Leaf304,Sensitive Strong,2 414 | s__Leaf59,Sensitive Strong,0 415 | s__Leaf177,Sensitive Strong,0 416 | s__Leaf127,Sensitive Strong,0 417 | s__Leaf61,Sensitive Strong,0 418 | s__Leaf202,Sensitive Strong,3 419 | s__Leaf131,Sensitive Strong,1 420 | s__Leaf272,Sensitive Strong,0 421 | s__Leaf145,Sensitive Strong,0 422 | s__Leaf245,Sensitive Strong,0 423 | s__Leaf359,Sensitive Strong,0 424 | s__Leaf394,Sensitive Strong,11 425 | s__Leaf404,Sensitive Strong,4 426 | s__Leaf285,Sensitive Strong,1 427 | s__Leaf148,Sensitive Strong,1 428 | s__Leaf141,Sensitive Strong,0 429 | s__Leaf137,Sensitive Strong,0 430 | s__Leaf167,Sensitive Strong,0 431 | s__Leaf194,Sensitive Strong,0 432 | s__Leaf201,Sensitive Strong,0 433 | s__Leaf465,Sensitive Strong,0 434 | s__Leaf78,Sensitive Strong,0 435 | s__Leaf83,Sensitive Strong,0 436 | s__Leaf16,Sensitive Strong,1 437 | s__Leaf291,Sensitive Strong,1 438 | s__Leaf32,Sensitive Strong,1 439 | s__Leaf69,Sensitive Strong,1 440 | s__Leaf289,Sensitive Strong,0 441 | s__Leaf13,Sensitive Strong,0 442 | s__Leaf139,Sensitive Strong,0 443 | s__Leaf176,Sensitive Strong,0 444 | s__Leaf203,Sensitive Strong,0 445 | s__Leaf254,Sensitive Strong,0 446 | s__Leaf313,Sensitive Strong,0 447 | s__Leaf405,Sensitive Strong,0 448 | s__Leaf53,Sensitive Strong,0 449 | s__Leaf68,Sensitive Strong,0 450 | s__Leaf70,Sensitive Strong,0 451 | s__Leaf407,Sensitive Strong,6 452 | s__Leaf28,Sensitive Strong,5 453 | s__Leaf357,Sensitive Strong,3 454 | s__Leaf374,Sensitive Strong,2 455 | s__Leaf44,Sensitive Strong,2 456 | s__Leaf395,Sensitive Strong,1 457 | s__Leaf122,Sensitive Strong,0 458 | s__Leaf125,Sensitive Strong,0 459 | s__Leaf23,Sensitive Strong,0 460 | s__Leaf93,Sensitive Strong,0 461 | s__Leaf250,Sensitive Strong,0 462 | s__Leaf191,Sensitive Strong,0 463 | s__Leaf21,Sensitive Strong,0 464 | s__Leaf280,Sensitive Strong,0 465 | s__Leaf337,Sensitive Strong,0 466 | s__Leaf121,Sensitive Strong,0 467 | s__Leaf129,Sensitive Strong,0 468 | s__Leaf161,Sensitive Strong,0 469 | s__Leaf170,Sensitive Strong,0 470 | s__Leaf262,Sensitive Strong,0 471 | s__Leaf264,Sensitive Strong,0 472 | s__Leaf306,Sensitive Strong,0 473 | s__Leaf48,Sensitive Strong,0 474 | s__Leaf76,Sensitive Strong,0 475 | s__Leaf326,Sensitive Strong,9 476 | s__Leaf41,Sensitive Strong,8 477 | s__Leaf401,Sensitive Strong,6 478 | s__Leaf205,Sensitive Strong,6 479 | s__Leaf242,Sensitive Strong,5 480 | s__Leaf62,Sensitive Strong,5 481 | s__Leaf38,Sensitive Strong,4 482 | s__Leaf33,Sensitive Strong,4 483 | s__Leaf198,Sensitive Strong,3 484 | s__Leaf17,Sensitive Strong,3 485 | s__Leaf180,Sensitive Strong,3 486 | s__Leaf189,Sensitive Strong,2 487 | s__Leaf208,Sensitive Strong,2 488 | s__Leaf34,Sensitive Strong,2 489 | s__Leaf443,Sensitive Strong,2 490 | s__Leaf1,Sensitive Strong,2 491 | s__Leaf234,Sensitive Strong,2 492 | s__Leaf369,Sensitive Strong,2 493 | s__Leaf307,Sensitive Strong,2 494 | s__Leaf42,Sensitive Strong,2 495 | s__Leaf8,Sensitive Strong,2 496 | s__Leaf226,Sensitive Strong,1 497 | s__Leaf400,Sensitive Strong,1 498 | s__Leaf89,Sensitive Strong,1 499 | s__Leaf186,Sensitive Strong,1 500 | s__Leaf335,Sensitive Strong,1 501 | s__Leaf37,Sensitive Strong,1 502 | s__Leaf5,Sensitive Strong,1 503 | s__Leaf67,Sensitive Strong,1 504 | s__Leaf29,Sensitive Strong,1 505 | s__Leaf380,Sensitive Strong,1 506 | s__Leaf459,Sensitive Strong,1 507 | s__Leaf64,Sensitive Strong,1 508 | s__Leaf9,Sensitive Strong,1 509 | s__Leaf220,Sensitive Strong,1 510 | s__Leaf25,Sensitive Strong,1 511 | s__Leaf22,Sensitive Strong,1 512 | s__Leaf3,Sensitive Strong,1 513 | s__Leaf334,Sensitive Strong,1 514 | s__Leaf453,Sensitive Strong,1 515 | s__Leaf446,Sensitive Strong,0 516 | s__Leaf347,Sensitive Strong,0 517 | s__Leaf113,Sensitive Strong,0 518 | s__Leaf351,Sensitive Strong,0 519 | s__Leaf111,Sensitive Strong,0 520 | s__Leaf117,Sensitive Strong,0 521 | s__Leaf72,Sensitive Strong,0 522 | s__Leaf341,Sensitive Strong,0 523 | s__Leaf92,Sensitive Strong,0 524 | s__Leaf132,Sensitive Strong,0 525 | s__Leaf123,Sensitive Strong,0 526 | s__Leaf151,Sensitive Strong,0 527 | s__Leaf339,Sensitive Strong,0 528 | s__Leaf344,Sensitive Strong,0 529 | s__Leaf363,Sensitive Strong,0 530 | s__Leaf4,Sensitive Strong,0 531 | s__Leaf10,Sensitive Strong,0 532 | s__Leaf100,Sensitive Strong,0 533 | s__Leaf267,Sensitive Strong,0 534 | s__Leaf294,Sensitive Strong,0 535 | s__Leaf343,Sensitive Strong,0 536 | s__Leaf384,Sensitive Strong,0 537 | s__Leaf420,Sensitive Strong,0 538 | s__Leaf427,Sensitive Strong,0 539 | s__Leaf436,Sensitive Strong,0 540 | s__Leaf456,Sensitive Strong,0 541 | s__Leaf466,Sensitive Strong,0 542 | s__Leaf84,Sensitive Strong,0 543 | s__Leaf90,Sensitive Strong,0 544 | s__Leaf102,Sensitive Strong,0 545 | s__Leaf106,Sensitive Strong,0 546 | s__Leaf112,Sensitive Strong,0 547 | s__Leaf155,Sensitive Strong,0 548 | s__Leaf20,Sensitive Strong,0 549 | s__Leaf225,Sensitive Strong,0 550 | s__Leaf230,Sensitive Strong,0 551 | s__Leaf258,Sensitive Strong,0 552 | s__Leaf320,Sensitive Strong,0 553 | s__Leaf325,Sensitive Strong,0 554 | s__Leaf350,Sensitive Strong,0 555 | s__Leaf354,Sensitive Strong,0 556 | s__Leaf396,Sensitive Strong,0 557 | s__Leaf414,Sensitive Strong,0 558 | s__Leaf416,Sensitive Strong,0 559 | s__Leaf87,Sensitive Strong,0 560 | s__Leaf91,Sensitive Strong,0 561 | s__Leaf99,Sensitive Strong,0 562 | s__Leaf172,Sensitive Strong,0 563 | s__Leaf185,Sensitive Strong,0 564 | s__Leaf24,Sensitive Strong,0 565 | s__Leaf263,Sensitive Strong,0 566 | s__Leaf283,Sensitive Strong,0 567 | s__Leaf299,Sensitive Strong,0 568 | s__Leaf314,Sensitive Strong,0 569 | s__Leaf361,Sensitive Strong,0 570 | s__Leaf399,Sensitive Strong,0 571 | s__Leaf412,Sensitive Strong,0 572 | s__Leaf460,Sensitive Strong,0 573 | s__Leaf7,Sensitive Strong,0 574 | s__Leaf86,Sensitive Strong,0 575 | s__Leaf108,Sensitive Strong,0 576 | s__Leaf118,Sensitive Strong,0 577 | s__Leaf119,Sensitive Strong,0 578 | s__Leaf160,Sensitive Strong,0 579 | s__Leaf179,Sensitive Strong,0 580 | s__Leaf183,Sensitive Strong,0 581 | s__Leaf231,Sensitive Strong,0 582 | s__Leaf244,Sensitive Strong,0 583 | s__Leaf248,Sensitive Strong,0 584 | s__Leaf26,Sensitive Strong,0 585 | s__Leaf265,Sensitive Strong,0 586 | s__Leaf296,Sensitive Strong,0 587 | s__Leaf321,Sensitive Strong,0 588 | s__Leaf386,Sensitive Strong,0 589 | s__Leaf391,Sensitive Strong,0 590 | s__Leaf415,Sensitive Strong,0 591 | s__Leaf85,Sensitive Strong,0 592 | s__Leaf88,Sensitive Strong,0 593 | s__Leaf182,Sensitive Weak,3 594 | s__Leaf98,Sensitive Weak,0 595 | s__Leaf434,Sensitive Weak,0 596 | s__Leaf58,Sensitive Weak,0 597 | s__Leaf15,Sensitive Weak,0 598 | s__Leaf49,Sensitive Weak,1 599 | s__Leaf2,Sensitive Weak,0 600 | s__Leaf408,Sensitive Weak,7 601 | s__Leaf75,Sensitive Weak,0 602 | s__Leaf82,Sensitive Weak,1 603 | s__Leaf196,Sensitive Weak,0 604 | s__Leaf154,Sensitive Weak,0 605 | s__Leaf11,Sensitive Weak,0 606 | s__Leaf126,Sensitive Weak,5 607 | s__Leaf130,Sensitive Weak,1 608 | s__Leaf187,Sensitive Weak,0 609 | s__Leaf30,Sensitive Weak,11 610 | s__Leaf304,Sensitive Weak,2 611 | s__Leaf59,Sensitive Weak,0 612 | s__Leaf177,Sensitive Weak,1 613 | s__Leaf127,Sensitive Weak,1 614 | s__Leaf61,Sensitive Weak,0 615 | s__Leaf202,Sensitive Weak,0 616 | s__Leaf131,Sensitive Weak,4 617 | s__Leaf272,Sensitive Weak,0 618 | s__Leaf145,Sensitive Weak,0 619 | s__Leaf245,Sensitive Weak,0 620 | s__Leaf359,Sensitive Weak,0 621 | s__Leaf394,Sensitive Weak,7 622 | s__Leaf404,Sensitive Weak,8 623 | s__Leaf285,Sensitive Weak,5 624 | s__Leaf148,Sensitive Weak,3 625 | s__Leaf141,Sensitive Weak,2 626 | s__Leaf137,Sensitive Weak,0 627 | s__Leaf167,Sensitive Weak,0 628 | s__Leaf194,Sensitive Weak,0 629 | s__Leaf201,Sensitive Weak,0 630 | s__Leaf465,Sensitive Weak,0 631 | s__Leaf78,Sensitive Weak,0 632 | s__Leaf83,Sensitive Weak,0 633 | s__Leaf16,Sensitive Weak,6 634 | s__Leaf291,Sensitive Weak,3 635 | s__Leaf32,Sensitive Weak,3 636 | s__Leaf69,Sensitive Weak,3 637 | s__Leaf289,Sensitive Weak,4 638 | s__Leaf13,Sensitive Weak,1 639 | s__Leaf139,Sensitive Weak,1 640 | s__Leaf176,Sensitive Weak,1 641 | s__Leaf203,Sensitive Weak,0 642 | s__Leaf254,Sensitive Weak,0 643 | s__Leaf313,Sensitive Weak,0 644 | s__Leaf405,Sensitive Weak,0 645 | s__Leaf53,Sensitive Weak,0 646 | s__Leaf68,Sensitive Weak,0 647 | s__Leaf70,Sensitive Weak,0 648 | s__Leaf407,Sensitive Weak,6 649 | s__Leaf28,Sensitive Weak,4 650 | s__Leaf357,Sensitive Weak,6 651 | s__Leaf374,Sensitive Weak,4 652 | s__Leaf44,Sensitive Weak,1 653 | s__Leaf395,Sensitive Weak,4 654 | s__Leaf122,Sensitive Weak,4 655 | s__Leaf125,Sensitive Weak,3 656 | s__Leaf23,Sensitive Weak,3 657 | s__Leaf93,Sensitive Weak,3 658 | s__Leaf250,Sensitive Weak,2 659 | s__Leaf191,Sensitive Weak,1 660 | s__Leaf21,Sensitive Weak,1 661 | s__Leaf280,Sensitive Weak,1 662 | s__Leaf337,Sensitive Weak,1 663 | s__Leaf121,Sensitive Weak,0 664 | s__Leaf129,Sensitive Weak,0 665 | s__Leaf161,Sensitive Weak,0 666 | s__Leaf170,Sensitive Weak,0 667 | s__Leaf262,Sensitive Weak,0 668 | s__Leaf264,Sensitive Weak,0 669 | s__Leaf306,Sensitive Weak,0 670 | s__Leaf48,Sensitive Weak,0 671 | s__Leaf76,Sensitive Weak,0 672 | s__Leaf326,Sensitive Weak,7 673 | s__Leaf41,Sensitive Weak,0 674 | s__Leaf401,Sensitive Weak,5 675 | s__Leaf205,Sensitive Weak,2 676 | s__Leaf242,Sensitive Weak,0 677 | s__Leaf62,Sensitive Weak,0 678 | s__Leaf38,Sensitive Weak,16 679 | s__Leaf33,Sensitive Weak,4 680 | s__Leaf198,Sensitive Weak,4 681 | s__Leaf17,Sensitive Weak,2 682 | s__Leaf180,Sensitive Weak,2 683 | s__Leaf189,Sensitive Weak,13 684 | s__Leaf208,Sensitive Weak,12 685 | s__Leaf34,Sensitive Weak,9 686 | s__Leaf443,Sensitive Weak,8 687 | s__Leaf1,Sensitive Weak,6 688 | s__Leaf234,Sensitive Weak,6 689 | s__Leaf369,Sensitive Weak,5 690 | s__Leaf307,Sensitive Weak,4 691 | s__Leaf42,Sensitive Weak,3 692 | s__Leaf8,Sensitive Weak,3 693 | s__Leaf226,Sensitive Weak,9 694 | s__Leaf400,Sensitive Weak,8 695 | s__Leaf89,Sensitive Weak,7 696 | s__Leaf186,Sensitive Weak,5 697 | s__Leaf335,Sensitive Weak,4 698 | s__Leaf37,Sensitive Weak,4 699 | s__Leaf5,Sensitive Weak,4 700 | s__Leaf67,Sensitive Weak,3 701 | s__Leaf29,Sensitive Weak,2 702 | s__Leaf380,Sensitive Weak,2 703 | s__Leaf459,Sensitive Weak,2 704 | s__Leaf64,Sensitive Weak,2 705 | s__Leaf9,Sensitive Weak,2 706 | s__Leaf220,Sensitive Weak,1 707 | s__Leaf25,Sensitive Weak,1 708 | s__Leaf22,Sensitive Weak,0 709 | s__Leaf3,Sensitive Weak,0 710 | s__Leaf334,Sensitive Weak,0 711 | s__Leaf453,Sensitive Weak,0 712 | s__Leaf446,Sensitive Weak,17 713 | s__Leaf347,Sensitive Weak,15 714 | s__Leaf113,Sensitive Weak,14 715 | s__Leaf351,Sensitive Weak,11 716 | s__Leaf111,Sensitive Weak,10 717 | s__Leaf117,Sensitive Weak,9 718 | s__Leaf72,Sensitive Weak,9 719 | s__Leaf341,Sensitive Weak,7 720 | s__Leaf92,Sensitive Weak,7 721 | s__Leaf132,Sensitive Weak,6 722 | s__Leaf123,Sensitive Weak,5 723 | s__Leaf151,Sensitive Weak,5 724 | s__Leaf339,Sensitive Weak,5 725 | s__Leaf344,Sensitive Weak,5 726 | s__Leaf363,Sensitive Weak,5 727 | s__Leaf4,Sensitive Weak,5 728 | s__Leaf10,Sensitive Weak,4 729 | s__Leaf100,Sensitive Weak,4 730 | s__Leaf267,Sensitive Weak,4 731 | s__Leaf294,Sensitive Weak,4 732 | s__Leaf343,Sensitive Weak,4 733 | s__Leaf384,Sensitive Weak,4 734 | s__Leaf420,Sensitive Weak,4 735 | s__Leaf427,Sensitive Weak,4 736 | s__Leaf436,Sensitive Weak,4 737 | s__Leaf456,Sensitive Weak,4 738 | s__Leaf466,Sensitive Weak,4 739 | s__Leaf84,Sensitive Weak,4 740 | s__Leaf90,Sensitive Weak,4 741 | s__Leaf102,Sensitive Weak,3 742 | s__Leaf106,Sensitive Weak,3 743 | s__Leaf112,Sensitive Weak,3 744 | s__Leaf155,Sensitive Weak,3 745 | s__Leaf20,Sensitive Weak,3 746 | s__Leaf225,Sensitive Weak,3 747 | s__Leaf230,Sensitive Weak,3 748 | s__Leaf258,Sensitive Weak,3 749 | s__Leaf320,Sensitive Weak,3 750 | s__Leaf325,Sensitive Weak,3 751 | s__Leaf350,Sensitive Weak,3 752 | s__Leaf354,Sensitive Weak,3 753 | s__Leaf396,Sensitive Weak,3 754 | s__Leaf414,Sensitive Weak,3 755 | s__Leaf416,Sensitive Weak,3 756 | s__Leaf87,Sensitive Weak,3 757 | s__Leaf91,Sensitive Weak,3 758 | s__Leaf99,Sensitive Weak,3 759 | s__Leaf172,Sensitive Weak,2 760 | s__Leaf185,Sensitive Weak,2 761 | s__Leaf24,Sensitive Weak,2 762 | s__Leaf263,Sensitive Weak,2 763 | s__Leaf283,Sensitive Weak,2 764 | s__Leaf299,Sensitive Weak,2 765 | s__Leaf314,Sensitive Weak,2 766 | s__Leaf361,Sensitive Weak,2 767 | s__Leaf399,Sensitive Weak,2 768 | s__Leaf412,Sensitive Weak,2 769 | s__Leaf460,Sensitive Weak,2 770 | s__Leaf7,Sensitive Weak,2 771 | s__Leaf86,Sensitive Weak,2 772 | s__Leaf108,Sensitive Weak,1 773 | s__Leaf118,Sensitive Weak,1 774 | s__Leaf119,Sensitive Weak,1 775 | s__Leaf160,Sensitive Weak,1 776 | s__Leaf179,Sensitive Weak,1 777 | s__Leaf183,Sensitive Weak,1 778 | s__Leaf231,Sensitive Weak,1 779 | s__Leaf244,Sensitive Weak,1 780 | s__Leaf248,Sensitive Weak,1 781 | s__Leaf26,Sensitive Weak,1 782 | s__Leaf265,Sensitive Weak,1 783 | s__Leaf296,Sensitive Weak,1 784 | s__Leaf321,Sensitive Weak,1 785 | s__Leaf386,Sensitive Weak,1 786 | s__Leaf391,Sensitive Weak,1 787 | s__Leaf415,Sensitive Weak,1 788 | s__Leaf85,Sensitive Weak,1 789 | s__Leaf88,Sensitive Weak,1 790 | -------------------------------------------------------------------------------- /data/Arabidopsis_leaf_microbiome/all_stain_taxonomy.csv: -------------------------------------------------------------------------------- 1 | Kindom,Phylum,Class,Order,Family,Genus,Isolation 2 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf11 3 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf121 4 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf122 5 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf125 6 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Oxalobacteraceae,Duganella,Leaf126 7 | Bacteria,Proteobacteria,Gammaproteobacteria,Pseudomonadales,Pseudomonadaceae,Pseudomonas,Leaf127 8 | Bacteria,Proteobacteria,Gammaproteobacteria,Pseudomonadales,Pseudomonadaceae,Pseudomonas,Leaf129 9 | Bacteria,Firmicutes,Bacilli,Bacillales,Bacillaceae,Bacillus,Leaf13 10 | Bacteria,Proteobacteria,Gammaproteobacteria,Pseudomonadales,Moraxellaceae,Acinetobacter,Leaf130 11 | Bacteria,Proteobacteria,Gammaproteobacteria,Xanthomonadales,Xanthomonadaceae,Xanthomonas,Leaf131 12 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Micrococcaceae,Arthrobacter,Leaf137 13 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Oxalobacteraceae,Massilia,Leaf139 14 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Micrococcaceae,Arthrobacter,Leaf141 15 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Micrococcaceae,Arthrobacter,Leaf145 16 | Bacteria,Proteobacteria,Gammaproteobacteria,Xanthomonadales,Xanthomonadaceae,Xanthomonas,Leaf148 17 | Bacteria,Proteobacteria,Gammaproteobacteria,Pseudomonadales,Pseudomonadaceae,Pseudomonas,Leaf15 18 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Curtobacterium,Leaf154 19 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf16 20 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Microbacterium,Leaf161 21 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf167 22 | Bacteria,Bacteroidetes,Sphingobacteriia,Sphingobacteriales,Sphingobacteriaceae,Pedobacter,Leaf170 23 | Bacteria,Bacteroidetes,Sphingobacteriia,Sphingobacteriales,Sphingobacteriaceae,Pedobacter,Leaf176 24 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Burkholderiaceae,Burkholderia,Leaf177 25 | Bacteria,Firmicutes,Bacilli,Bacillales,Paenibacillaceae,Brevibacillus,Leaf182 26 | Bacteria,Firmicutes,Bacilli,Bacillales,Bacillales,Exiguobacterium,Leaf187 27 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Comamonadaceae,Acidovorax,Leaf191 28 | Bacteria,Bacteroidetes,Sphingobacteriia,Sphingobacteriales,Sphingobacteriaceae,Pedobacter,Leaf194 29 | Bacteria,Firmicutes,Bacilli,Bacillales,Bacillales,Exiguobacterium,Leaf196 30 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Novosphingobium,Leaf2 31 | Bacteria,Bacteroidetes,Flavobacteriia,Flavobacteriales,Flavobacteriaceae,Chryseobacterium,Leaf201 32 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf202 33 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Microbacterium,Leaf203 34 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf21 35 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf23 36 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardioidaceae,Aeromicrobium,Leaf245 37 | Bacteria,Bacteroidetes,Sphingobacteriia,Sphingobacteriales,Sphingobacteriaceae,Pedobacter,Leaf250 38 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Frigoribacterium,Leaf254 39 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf262 40 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Leifsonia,Leaf264 41 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardioidaceae,Aeromicrobium,Leaf272 42 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf28 43 | Bacteria,Proteobacteria,Alphaproteobacteria,Caulobacterales,Caulobacteraceae,Brevundimonas,Leaf280 44 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardioidaceae,Nocardioides,Leaf285 45 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardioidaceae,Aeromicrobium,Leaf289 46 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardioidaceae,Aeromicrobium,Leaf291 47 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf30 48 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Frondihabitans,Leaf304 49 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf306 50 | Bacteria,Bacteroidetes,Flavobacteriia,Flavobacteriales,Flavobacteriaceae,Chryseobacterium,Leaf313 51 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf32 52 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Micrococcaceae,Arthrobacter,Leaf337 53 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf357 54 | Bacteria,Bacteroidetes,Flavobacteriia,Flavobacteriales,Flavobacteriaceae,Flavobacterium,Leaf359 55 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardioidaceae,Nocardioides,Leaf374 56 | Bacteria,Bacteroidetes,Flavobacteriia,Flavobacteriales,Flavobacteriaceae,Chryseobacterium,Leaf394 57 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Cellulomonadaceae,Cellulomonas,Leaf395 58 | Bacteria,Bacteroidetes,Flavobacteriia,Flavobacteriales,Flavobacteriaceae,Chryseobacterium,Leaf404 59 | Bacteria,Bacteroidetes,Flavobacteriia,Flavobacteriales,Flavobacteriaceae,Chryseobacterium,Leaf405 60 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf407 61 | Bacteria,Proteobacteria,Betaproteobacteria,Methylophilales,Methylophilaceae,Methylophilus,Leaf408 62 | Bacteria,Proteobacteria,Gammaproteobacteria,Pseudomonadales,Pseudomonadaceae,Pseudomonas,Leaf434 63 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Frigoribacterium,Leaf44 64 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf465 65 | Bacteria,Proteobacteria,Gammaproteobacteria,Pseudomonadales,Pseudomonadaceae,Pseudomonas,Leaf48 66 | Bacteria,Firmicutes,Bacilli,Bacillales,Bacillaceae,Bacillus,Leaf49 67 | Bacteria,Proteobacteria,Gammaproteobacteria,Enterobacteriales,Enterobacteriaceae,Erwinia,Leaf53 68 | Bacteria,Proteobacteria,Gammaproteobacteria,Pseudomonadales,Pseudomonadaceae,Pseudomonas,Leaf58 69 | Bacteria,Proteobacteria,Gammaproteobacteria,Pseudomonadales,Pseudomonadaceae,Pseudomonas,Leaf59 70 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Oxalobacteraceae,Duganella,Leaf61 71 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf68 72 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Micrococcaceae,Arthrobacter,Leaf69 73 | Bacteria,Proteobacteria,Gammaproteobacteria,Xanthomonadales,Xanthomonadaceae,Stenotrophomonas,Leaf70 74 | Bacteria,Firmicutes,Bacilli,Bacillales,Bacillaceae,Bacillus,Leaf75 75 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Comamonadaceae,Acidovorax,Leaf76 76 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Comamonadaceae,Acidovorax,Leaf78 77 | Bacteria,Bacteroidetes,Flavobacteriia,Flavobacteriales,Flavobacteriaceae,Flavobacterium,Leaf82 78 | Bacteria,Proteobacteria,Gammaproteobacteria,Pseudomonadales,Pseudomonadaceae,Pseudomonas,Leaf83 79 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf93 80 | Bacteria,Proteobacteria,Gammaproteobacteria,Pseudomonadales,Pseudomonadaceae,Pseudomonas,Leaf98 81 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Rathayibacter,Leaf294 82 | Bacteria,Deinococcus-Thermus,Deinococci,Deinococcales,Deinococcaceae,Deinococcus,Leaf326 83 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf341 84 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Bradyrhizobiaceae,Bosea,Leaf344 85 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Microbacterium,Leaf347 86 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Microbacterium,Leaf351 87 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Comamonadaceae,Acidovorax,Leaf400 88 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Bradyrhizobiaceae,Bradyrhizobium,Leaf401 89 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf456 90 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf111 91 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf113 92 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf226 93 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Leifsonia,Leaf325 94 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf339 95 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf38 96 | Bacteria,Bacteroidetes,Sphingobacteriia,Sphingobacteriales,Sphingobacteriaceae,Pedobacter,Leaf41 97 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf89 98 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf92 99 | Bacteria,Firmicutes,Bacilli,Bacillales,Paenibacillaceae,Paenibacillus,Leaf72 100 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Comamonadaceae,Acidovorax,Leaf84 101 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Geodermatophilaceae,Geodermatophilus,Leaf369 102 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardioidaceae,Marmoricola,Leaf446 103 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Plantibacter,Leaf1 104 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf10 105 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf208 106 | Bacteria,Bacteroidetes,Cytophagia,Cytophagales,Cytophagaceae,Dyadobacter,Leaf189 107 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Micrococcaceae,Arthrobacter,Leaf234 108 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf34 109 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf100 110 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf102 111 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf106 112 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf112 113 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf117 114 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf123 115 | Bacteria,Bacteroidetes,Sphingobacteriia,Sphingobacteriales,Sphingobacteriaceae,Pedobacter,Leaf132 116 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Microbacterium,Leaf151 117 | Bacteria,Bacteroidetes,Flavobacteriia,Flavobacteriales,Flavobacteriaceae,Chryseobacterium,Leaf180 118 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf198 119 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf205 120 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Comamonadaceae,Variovorax,Leaf267 121 | Bacteria,Proteobacteria,Betaproteobacteria,Methylophilales,Methylophilaceae,Methylophilus,Leaf414 122 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Hyphomicrobiaceae,Devosia,Leaf420 123 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Aurantimonadaceae,Aurantimonas,Leaf443 124 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf466 125 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf86 126 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf87 127 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf88 128 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf90 129 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf91 130 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf99 131 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf118 132 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Geodermatophilaceae,Blastococcus,Leaf380 133 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Frigoribacterium,Leaf8 134 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf4 135 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf155 136 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf361 137 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Aurantimonadaceae,Aurantimonas,Leaf427 138 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Microbacterium,Leaf436 139 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Comamonadaceae,Acidovorax,Leaf160 140 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf17 141 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Clavibacter,Leaf172 142 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Curtobacterium,Leaf183 143 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Rathayibacter,Leaf185 144 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Frigoribacterium,Leaf186 145 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf20 146 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf22 147 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Comamonadaceae,Variovorax,Leaf220 148 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardiaceae,Rhodococcus,Leaf225 149 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf230 150 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf24 151 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf242 152 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Agreia,Leaf244 153 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Rathayibacter,Leaf248 154 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf25 155 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardiaceae,Rhodococcus,Leaf258 156 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Clavibacter,Leaf263 157 | Bacteria,Proteobacteria,Betaproteobacteria,Burkholderiales,Comamonadaceae,Pseudorhodoferax,Leaf265 158 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Agreia,Leaf283 159 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf29 160 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Sanguibacteraceae,Sanguibacter,Leaf3 161 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardioidaceae,Nocardioides,Leaf307 162 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf33 163 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Agreia,Leaf335 164 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf343 165 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardioidaceae,Aeromicrobium,Leaf350 166 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardiaceae,Williamsia,Leaf354 167 | Bacteria,Proteobacteria,Alphaproteobacteria,Caulobacterales,Caulobacteraceae,Brevundimonas,Leaf363 168 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf37 169 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf386 170 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf391 171 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Bradyrhizobiaceae,Bradyrhizobium,Leaf396 172 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf399 173 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf42 174 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf453 175 | Bacteria,Proteobacteria,Betaproteobacteria,Methylophilales,Methylophilaceae,Methylophilus,Leaf459 176 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Aurantimonadaceae,Aurantimonas,Leaf460 177 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf5 178 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf62 179 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Hyphomicrobiaceae,Devosia,Leaf64 180 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf67 181 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Nocardiaceae,Rhodococcus,Leaf7 182 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf85 183 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf9 184 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Plantibacter,Leaf314 185 | Bacteria,Proteobacteria,Betaproteobacteria,Methylophilales,Methylophilaceae,Methylophilus,Leaf416 186 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Rathayibacter,Leaf299 187 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Rathayibacter,Leaf296 188 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Microbacterium,Leaf320 189 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf384 190 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf412 191 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Microbacterium,Leaf179 192 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Rhizobiaceae,Rhizobium,Leaf321 193 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingobium,Leaf26 194 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Microbacteriaceae,Frigoribacterium,Leaf415 195 | Bacteria,Actinobacteria,Actinobacteria,Actinomycetales,Cellulomonadaceae,Cellulomonas,Leaf334 196 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf108 197 | Bacteria,Proteobacteria,Alphaproteobacteria,Rhizobiales,Methylobacteriaceae,Methylobacterium,Leaf119 198 | Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Sphingomonas,Leaf231 199 | Bacteria,Firmicutes,Bacilli,Bacillales,Bacillaceae,Bacillus,Leaf406 200 | -------------------------------------------------------------------------------- /data/Arabidopsis_leaf_microbiome/stain_tippoint.csv: -------------------------------------------------------------------------------- 1 | Isolation,Taxa,Level 2 | s__Leaf13,Firmicutes,Phylum 3 | s__Leaf137,Actinobacteria,Phylum 4 | s__Leaf141,Actinobacteria,Phylum 5 | s__Leaf145,Actinobacteria,Phylum 6 | s__Leaf154,Actinobacteria,Phylum 7 | s__Leaf161,Actinobacteria,Phylum 8 | s__Leaf170,Bacteroidetes,Phylum 9 | s__Leaf176,Bacteroidetes,Phylum 10 | s__Leaf182,Firmicutes,Phylum 11 | s__Leaf187,Firmicutes,Phylum 12 | s__Leaf194,Bacteroidetes,Phylum 13 | s__Leaf196,Firmicutes,Phylum 14 | s__Leaf201,Bacteroidetes,Phylum 15 | s__Leaf203,Actinobacteria,Phylum 16 | s__Leaf245,Actinobacteria,Phylum 17 | s__Leaf250,Bacteroidetes,Phylum 18 | s__Leaf254,Actinobacteria,Phylum 19 | s__Leaf264,Actinobacteria,Phylum 20 | s__Leaf272,Actinobacteria,Phylum 21 | s__Leaf285,Actinobacteria,Phylum 22 | s__Leaf289,Actinobacteria,Phylum 23 | s__Leaf291,Actinobacteria,Phylum 24 | s__Leaf304,Actinobacteria,Phylum 25 | s__Leaf313,Bacteroidetes,Phylum 26 | s__Leaf337,Actinobacteria,Phylum 27 | s__Leaf359,Bacteroidetes,Phylum 28 | s__Leaf374,Actinobacteria,Phylum 29 | s__Leaf394,Bacteroidetes,Phylum 30 | s__Leaf395,Actinobacteria,Phylum 31 | s__Leaf404,Bacteroidetes,Phylum 32 | s__Leaf405,Bacteroidetes,Phylum 33 | s__Leaf44,Actinobacteria,Phylum 34 | s__Leaf49,Firmicutes,Phylum 35 | s__Leaf69,Actinobacteria,Phylum 36 | s__Leaf75,Firmicutes,Phylum 37 | s__Leaf82,Bacteroidetes,Phylum 38 | s__Leaf294,Actinobacteria,Phylum 39 | s__Leaf326,Deinococcus-Thermus,Phylum 40 | s__Leaf347,Actinobacteria,Phylum 41 | s__Leaf351,Actinobacteria,Phylum 42 | s__Leaf325,Actinobacteria,Phylum 43 | s__Leaf41,Bacteroidetes,Phylum 44 | s__Leaf72,Firmicutes,Phylum 45 | s__Leaf369,Actinobacteria,Phylum 46 | s__Leaf446,Actinobacteria,Phylum 47 | s__Leaf1,Actinobacteria,Phylum 48 | s__Leaf189,Bacteroidetes,Phylum 49 | s__Leaf234,Actinobacteria,Phylum 50 | s__Leaf132,Bacteroidetes,Phylum 51 | s__Leaf151,Actinobacteria,Phylum 52 | s__Leaf180,Bacteroidetes,Phylum 53 | s__Leaf380,Actinobacteria,Phylum 54 | s__Leaf8,Actinobacteria,Phylum 55 | s__Leaf436,Actinobacteria,Phylum 56 | s__Leaf172,Actinobacteria,Phylum 57 | s__Leaf183,Actinobacteria,Phylum 58 | s__Leaf185,Actinobacteria,Phylum 59 | s__Leaf186,Actinobacteria,Phylum 60 | s__Leaf225,Actinobacteria,Phylum 61 | s__Leaf244,Actinobacteria,Phylum 62 | s__Leaf248,Actinobacteria,Phylum 63 | s__Leaf258,Actinobacteria,Phylum 64 | s__Leaf263,Actinobacteria,Phylum 65 | s__Leaf283,Actinobacteria,Phylum 66 | s__Leaf3,Actinobacteria,Phylum 67 | s__Leaf307,Actinobacteria,Phylum 68 | s__Leaf335,Actinobacteria,Phylum 69 | s__Leaf350,Actinobacteria,Phylum 70 | s__Leaf354,Actinobacteria,Phylum 71 | s__Leaf7,Actinobacteria,Phylum 72 | s__Leaf314,Actinobacteria,Phylum 73 | s__Leaf299,Actinobacteria,Phylum 74 | s__Leaf296,Actinobacteria,Phylum 75 | s__Leaf320,Actinobacteria,Phylum 76 | s__Leaf179,Actinobacteria,Phylum 77 | s__Leaf415,Actinobacteria,Phylum 78 | s__Leaf334,Actinobacteria,Phylum 79 | s__Leaf406,Firmicutes,Phylum 80 | s__Leaf11,Alphaproteobacteria,Class 81 | s__Leaf121,Alphaproteobacteria,Class 82 | s__Leaf122,Alphaproteobacteria,Class 83 | s__Leaf125,Alphaproteobacteria,Class 84 | s__Leaf126,Betaproteobacteria,Class 85 | s__Leaf127,Gammaproteobacteria,Class 86 | s__Leaf129,Gammaproteobacteria,Class 87 | s__Leaf130,Gammaproteobacteria,Class 88 | s__Leaf131,Gammaproteobacteria,Class 89 | s__Leaf139,Betaproteobacteria,Class 90 | s__Leaf148,Gammaproteobacteria,Class 91 | s__Leaf15,Gammaproteobacteria,Class 92 | s__Leaf16,Alphaproteobacteria,Class 93 | s__Leaf167,Alphaproteobacteria,Class 94 | s__Leaf177,Betaproteobacteria,Class 95 | s__Leaf191,Betaproteobacteria,Class 96 | s__Leaf2,Alphaproteobacteria,Class 97 | s__Leaf202,Alphaproteobacteria,Class 98 | s__Leaf21,Alphaproteobacteria,Class 99 | s__Leaf23,Alphaproteobacteria,Class 100 | s__Leaf262,Alphaproteobacteria,Class 101 | s__Leaf28,Alphaproteobacteria,Class 102 | s__Leaf280,Alphaproteobacteria,Class 103 | s__Leaf30,Alphaproteobacteria,Class 104 | s__Leaf306,Alphaproteobacteria,Class 105 | s__Leaf32,Alphaproteobacteria,Class 106 | s__Leaf357,Alphaproteobacteria,Class 107 | s__Leaf407,Alphaproteobacteria,Class 108 | s__Leaf408,Betaproteobacteria,Class 109 | s__Leaf434,Gammaproteobacteria,Class 110 | s__Leaf465,Alphaproteobacteria,Class 111 | s__Leaf48,Gammaproteobacteria,Class 112 | s__Leaf53,Gammaproteobacteria,Class 113 | s__Leaf58,Gammaproteobacteria,Class 114 | s__Leaf59,Gammaproteobacteria,Class 115 | s__Leaf61,Betaproteobacteria,Class 116 | s__Leaf68,Alphaproteobacteria,Class 117 | s__Leaf70,Gammaproteobacteria,Class 118 | s__Leaf76,Betaproteobacteria,Class 119 | s__Leaf78,Betaproteobacteria,Class 120 | s__Leaf83,Gammaproteobacteria,Class 121 | s__Leaf93,Alphaproteobacteria,Class 122 | s__Leaf98,Gammaproteobacteria,Class 123 | s__Leaf341,Alphaproteobacteria,Class 124 | s__Leaf344,Alphaproteobacteria,Class 125 | s__Leaf400,Betaproteobacteria,Class 126 | s__Leaf401,Alphaproteobacteria,Class 127 | s__Leaf456,Alphaproteobacteria,Class 128 | s__Leaf111,Alphaproteobacteria,Class 129 | s__Leaf113,Alphaproteobacteria,Class 130 | s__Leaf226,Alphaproteobacteria,Class 131 | s__Leaf339,Alphaproteobacteria,Class 132 | s__Leaf38,Alphaproteobacteria,Class 133 | s__Leaf89,Alphaproteobacteria,Class 134 | s__Leaf92,Alphaproteobacteria,Class 135 | s__Leaf84,Betaproteobacteria,Class 136 | s__Leaf10,Alphaproteobacteria,Class 137 | s__Leaf208,Alphaproteobacteria,Class 138 | s__Leaf34,Alphaproteobacteria,Class 139 | s__Leaf100,Alphaproteobacteria,Class 140 | s__Leaf102,Alphaproteobacteria,Class 141 | s__Leaf106,Alphaproteobacteria,Class 142 | s__Leaf112,Alphaproteobacteria,Class 143 | s__Leaf117,Alphaproteobacteria,Class 144 | s__Leaf123,Alphaproteobacteria,Class 145 | s__Leaf198,Alphaproteobacteria,Class 146 | s__Leaf205,Alphaproteobacteria,Class 147 | s__Leaf267,Betaproteobacteria,Class 148 | s__Leaf414,Betaproteobacteria,Class 149 | s__Leaf420,Alphaproteobacteria,Class 150 | s__Leaf443,Alphaproteobacteria,Class 151 | s__Leaf466,Alphaproteobacteria,Class 152 | s__Leaf86,Alphaproteobacteria,Class 153 | s__Leaf87,Alphaproteobacteria,Class 154 | s__Leaf88,Alphaproteobacteria,Class 155 | s__Leaf90,Alphaproteobacteria,Class 156 | s__Leaf91,Alphaproteobacteria,Class 157 | s__Leaf99,Alphaproteobacteria,Class 158 | s__Leaf118,Alphaproteobacteria,Class 159 | s__Leaf4,Alphaproteobacteria,Class 160 | s__Leaf155,Alphaproteobacteria,Class 161 | s__Leaf361,Alphaproteobacteria,Class 162 | s__Leaf427,Alphaproteobacteria,Class 163 | s__Leaf160,Betaproteobacteria,Class 164 | s__Leaf17,Alphaproteobacteria,Class 165 | s__Leaf20,Alphaproteobacteria,Class 166 | s__Leaf22,Alphaproteobacteria,Class 167 | s__Leaf220,Betaproteobacteria,Class 168 | s__Leaf230,Alphaproteobacteria,Class 169 | s__Leaf24,Alphaproteobacteria,Class 170 | s__Leaf242,Alphaproteobacteria,Class 171 | s__Leaf25,Alphaproteobacteria,Class 172 | s__Leaf265,Betaproteobacteria,Class 173 | s__Leaf29,Alphaproteobacteria,Class 174 | s__Leaf33,Alphaproteobacteria,Class 175 | s__Leaf343,Alphaproteobacteria,Class 176 | s__Leaf363,Alphaproteobacteria,Class 177 | s__Leaf37,Alphaproteobacteria,Class 178 | s__Leaf386,Alphaproteobacteria,Class 179 | s__Leaf391,Alphaproteobacteria,Class 180 | s__Leaf396,Alphaproteobacteria,Class 181 | s__Leaf399,Alphaproteobacteria,Class 182 | s__Leaf42,Alphaproteobacteria,Class 183 | s__Leaf453,Alphaproteobacteria,Class 184 | s__Leaf459,Betaproteobacteria,Class 185 | s__Leaf460,Alphaproteobacteria,Class 186 | s__Leaf5,Alphaproteobacteria,Class 187 | s__Leaf62,Alphaproteobacteria,Class 188 | s__Leaf64,Alphaproteobacteria,Class 189 | s__Leaf67,Alphaproteobacteria,Class 190 | s__Leaf85,Alphaproteobacteria,Class 191 | s__Leaf9,Alphaproteobacteria,Class 192 | s__Leaf416,Betaproteobacteria,Class 193 | s__Leaf384,Alphaproteobacteria,Class 194 | s__Leaf412,Alphaproteobacteria,Class 195 | s__Leaf321,Alphaproteobacteria,Class 196 | s__Leaf26,Alphaproteobacteria,Class 197 | s__Leaf108,Alphaproteobacteria,Class 198 | s__Leaf119,Alphaproteobacteria,Class 199 | s__Leaf231,Alphaproteobacteria,Class 200 | -------------------------------------------------------------------------------- /data/HMP_tree/barplot_attr.csv: -------------------------------------------------------------------------------- 1 | ID,Sites,HigherAbundance 2 | t637000026,Stool (prevalence),0.1322531 3 | t637000046,Vagina (prevalence),0.035 4 | t637000077,Stool (prevalence),0.035 5 | t637000092,Stool (prevalence),0.035 6 | t637000095,Stool (prevalence),0.035 7 | t637000127,Plaque (prevalence),0.035 8 | t637000163,Stool (prevalence),0.035 9 | t637000203,Tongue (prevalence),0.035 10 | t637000221,Vagina (prevalence),0.035 11 | t637000226,Stool (prevalence),0.035 12 | t637000227,Stool (prevalence),0.035 13 | t637000271,Stool (prevalence),0.035 14 | t637000281,Skin (prevalence),1.7287928 15 | t637000284,Stool (prevalence),0.035 16 | t637000302,Tongue (prevalence),0.035 17 | t637000327,Plaque (prevalence),0.0384153 18 | t637000332,Vagina (prevalence),0.0789712 19 | t638341112,Stool (prevalence),0.035 20 | t638341158,Stool (prevalence),0.035 21 | t638341196,Stool (prevalence),0.035 22 | t638341202,Stool (prevalence),0.035 23 | t639279312,Stool (prevalence),0.035 24 | t639633010,Stool (prevalence),0.0418075 25 | t639633027,Stool (prevalence),0.035 26 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(prevalence),0.1643698 50 | t640963046,Stool (prevalence),0.035 51 | t640963057,Stool (prevalence),0.035 52 | t640963058,Tongue (prevalence),0.13555815 53 | t641228489,Stool (prevalence),0.035 54 | t641228495,Stool (prevalence),0.035 55 | t641228498,Plaque (prevalence),0.035 56 | t641380421,Tongue (prevalence),0.035 57 | t641380422,Stool (prevalence),0.035 58 | t641380427,Stool (prevalence),0.035 59 | t641380428,Stool (prevalence),0.035 60 | t641380447,Stool (prevalence),0.21505365 61 | t641522636,Stool (prevalence),0.035 62 | t641522638,Stool (prevalence),0.035 63 | t641522641,Stool (prevalence),0.035 64 | t641522650,Stool (prevalence),0.035 65 | t641736113,Stool (prevalence),0.035 66 | t641736133,Stool (prevalence),0.035 67 | t641736156,Stool (prevalence),0.035 68 | t641736171,Stool (prevalence),0.035 69 | t641736189,Stool (prevalence),0.035 70 | t641736193,Stool (prevalence),0.035 71 | t641736196,Stool (prevalence),0.69204345 72 | t641736197,Stool (prevalence),0.035 73 | t641736205,Stool (prevalence),1.0281943 74 | t641736227,Stool (prevalence),0.035 75 | t641736271,Stool (prevalence),0.035 76 | t642555104,Stool (prevalence),0.1756692 77 | t642555107,Stool (prevalence),0.035 78 | t642555133,Stool (prevalence),0.035 79 | t642555148,Tongue (prevalence),0.035 80 | t642555160,Stool (prevalence),0.035 81 | t642555169,Stool (prevalence),0.035 82 | t642791604,Stool (prevalence),0.0409892 83 | t642791613,Stool (prevalence),0.08686685 84 | t642791621,Stool (prevalence),0.0675612 85 | t642979305,Plaque (prevalence),0.34347635 86 | t642979306,Skin (prevalence),0.035 87 | t642979312,Stool (prevalence),0.035 88 | t642979313,Stool (prevalence),0.035 89 | t642979316,Stool (prevalence),0.035 90 | t642979319,Stool (prevalence),0.3462326 91 | t642979320,Stool (prevalence),0.035 92 | t642979321,Stool (prevalence),0.035 93 | t642979351,Stool (prevalence),0.1613409 94 | t642979356,Stool (prevalence),0.1223558 95 | t642979358,Stool (prevalence),0.07141785 96 | 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(prevalence),0.035 120 | t643886055,Vagina (prevalence),0.035 121 | t643886057,Stool (prevalence),0.035 122 | t643886058,Nose (prevalence),2.1912912 123 | t643886063,Vagina (prevalence),0.035 124 | t643886070,Plaque (prevalence),0.035 125 | t643886074,Tongue (prevalence),0.33143285 126 | t643886084,Nose (prevalence),0.1159837 127 | t643886103,Stool (prevalence),0.035 128 | t643886104,Tongue (prevalence),0.1089571 129 | t643886107,Stool (prevalence),0.035 130 | t643886109,Stool (prevalence),0.035 131 | t643886110,Stool (prevalence),0.035 132 | t643886111,Stool (prevalence),0.31685255 133 | t643886112,Stool (prevalence),0.035 134 | t643886113,Plaque (prevalence),0.303856 135 | t643886116,Stool (prevalence),0.03798865 136 | t643886139,Stool (prevalence),0.035 137 | t643886142,Stool (prevalence),0.035 138 | t643886143,Stool (prevalence),0.035 139 | t643886145,Stool (prevalence),0.035 140 | t643886146,Stool (prevalence),0.035 141 | t643886148,Plaque (prevalence),0.0749924 142 | t643886150,Plaque (prevalence),0.7126903 143 | t643886151,Cheek (prevalence),0.035 144 | t643886181,Plaque (prevalence),0.035 145 | t643886188,Plaque (prevalence),0.0708568 146 | t643886193,Plaque (prevalence),0.1497888 147 | t643886194,Tongue (prevalence),0.2289952 148 | t643886197,Stool (prevalence),0.035 149 | t643886198,Tongue (prevalence),0.8942367 150 | t643886199,Stool (prevalence),0.035 151 | t643886200,Stool (prevalence),1.60445565 152 | t643886203,Stool (prevalence),0.035 153 | t643886206,Stool (prevalence),0.035 154 | t643886208,Plaque (prevalence),0.05481735 155 | t643886217,Vagina (prevalence),3.4955655 156 | t644736324,Plaque (prevalence),0.27294925 157 | t644736327,Tongue (prevalence),0.0719936 158 | t644736346,Plaque (prevalence),0.035 159 | t644736358,Stool (prevalence),0.035 160 | t644736366,Stool (prevalence),0.1200542 161 | t644736367,Stool (prevalence),0.59744125 162 | t644736381,Stool (prevalence),0.035 163 | t644736382,Stool (prevalence),0.035 164 | t644736384,Plaque (prevalence),0.1122373 165 | t644736390,Skin (prevalence),0.035 166 | t645058705,Cheek (prevalence),0.035 167 | t645058712,Vagina (prevalence),3.3628546 168 | t645058719,Nose (prevalence),0.07586565 169 | t645058720,Plaque (prevalence),0.0618765 170 | t645058738,Plaque (prevalence),0.035 171 | t645058748,Plaque (prevalence),0.33075665 172 | t645058761,Stool (prevalence),0.035 173 | t645058788,Stool (prevalence),0.035 174 | t645058800,Tongue (prevalence),0.6114507 175 | t645058825,Skin (prevalence),0.035 176 | t645058834,Cheek (prevalence),0.5328302 177 | t645058865,Stool (prevalence),0.035 178 | t645951802,Plaque (prevalence),0.035 179 | t645951804,Stool (prevalence),0.035 180 | t645951808,Plaque (prevalence),0.15132985 181 | t645951810,Skin (prevalence),0.035 182 | t645951817,Tongue (prevalence),0.0713286 183 | t645951819,Plaque (prevalence),0.13372415 184 | t645951825,Stool (prevalence),0.035 185 | t645951831,Stool (prevalence),0.4400445 186 | t645951833,Stool 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t647000302,Stool (prevalence),0.035 233 | t647000331,Plaque (prevalence),0.4522273 234 | t647533146,Stool (prevalence),0.035 235 | t647533156,Stool (prevalence),0.035 236 | t647533172,Cheek (prevalence),0.1436659 237 | t647533176,Vagina (prevalence),3.4997018 238 | t647533178,Stool (prevalence),0.035 239 | t647533181,Stool (prevalence),0.035 240 | t647533186,Plaque (prevalence),0.035 241 | t647533194,Stool (prevalence),0.035 242 | t647533210,Tongue (prevalence),0.035 243 | t648028005,Plaque (prevalence),0.035 244 | t648028010,Stool (prevalence),0.035 245 | t648028018,Stool (prevalence),0.035 246 | t648028033,Stool (prevalence),0.035 247 | t648028043,Stool (prevalence),0.035 248 | t648028047,Plaque (prevalence),0.035 249 | t648028051,Tongue (prevalence),0.7506632 250 | t648028055,Cheek (prevalence),0.035 251 | t648276633,Skin (prevalence),0.035 252 | t648276634,Plaque (prevalence),1.32123915 253 | t648276674,Skin (prevalence),0.31030615 254 | t648276682,Vagina (prevalence),3.3675978 255 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t649989999,Tongue (prevalence),0.09095345 301 | t649990001,Plaque (prevalence),0.035 302 | t649990003,Tongue (prevalence),0.3424806 303 | t649990004,Plaque (prevalence),0.07084315 304 | t649990007,Tongue (prevalence),0.27167315 305 | t649990011,Tongue (prevalence),0.0372757 306 | t649990014,Plaque (prevalence),0.47115705 307 | t649990016,Cheek (prevalence),0.27710235 308 | t649990021,Stool (prevalence),0.1999088 309 | t649990026,Stool (prevalence),0.035 310 | t650377901,Skin (prevalence),0.035 311 | t650377904,Stool (prevalence),0.2573032 312 | t650377925,Stool (prevalence),0.035 313 | t650377929,Stool (prevalence),0.035 314 | t650377938,Stool (prevalence),0.2355206 315 | t650377943,Stool (prevalence),0.035 316 | t650377944,Cheek (prevalence),0.4919257 317 | t650377954,Stool (prevalence),0.035 318 | t650377958,Stool (prevalence),0.035 319 | t650377963,Stool (prevalence),0.035 320 | t650377966,Stool (prevalence),0.33431195 321 | t650377974,Stool (prevalence),0.035 322 | t650377975,Stool (prevalence),0.035 323 | t650633000,Stool (prevalence),0.035 324 | t650716045,Stool (prevalence),0.035 325 | t650716089,Tongue (prevalence),0.7958867 326 | t651053005,Stool (prevalence),0.035 327 | t651053029,Stool (prevalence),0.035 328 | t651053056,Stool (prevalence),0.035 329 | t651053058,Skin (prevalence),3.47356625 330 | t651053073,Tongue (prevalence),0.49160055 331 | t651324009,Skin (prevalence),0.035 332 | t651324012,Stool (prevalence),1.12855925 333 | t651324039,Tongue (prevalence),1.75505365 334 | -------------------------------------------------------------------------------- /data/HMP_tree/hmptree.nwk: -------------------------------------------------------------------------------- 1 | ((t640427121:0.62306,t637000163:0.86427)1.00:1.20714,((t637000327:0.43426,(t649990026:0.44157,t645951869:0.42069)0.82:0.13553)1.00:2.28724,((((((t646206254:0.25238,(t645951859:0.05372,t646206275:0.05447)1.00:0.20326)1.00:0.22069,(t645951804:0.43651,(t647000254:0.08827,t645951848:0.09514)1.00:0.49290)0.76:0.12629)Fusobacterium1.00:0.57061,(t646311956:0.94182,(t647000268:0.25552,(t644736384:0.05250,t645951860:0.04949)1.00:0.25915)1.00:0.26943)1.00:0.55191)1.00:1.20558,((((t645951833:0.45158,t649989928:0.49364)1.00:0.86254,(t649989971:0.77561,(t648276753:0.08735,(t647000331:0.04084,t643886074:0.03151)1.00:0.07723)Veillonella1.00:0.87508)0.85:0.20223)1.00:0.34970,(t646311901:1.24020,(t650377958:0.64183,(t645951802:0.45313,(t642979367:0.31026,(t649989996:0.13520,(t645058738:0.18190,t645951808:0.12394)0.98:0.06557)1.00:0.46726)Selenomonas1.00:0.13201)1.00:0.24998)1.00:0.42320)0.79:0.12649)1.00:0.64941,(((((t645058834:0.12489,t649989952:0.13364)1.00:1.27427,(t650377974:0.24803,(t637000284:0.21116,(t646862342:0.17560,((t645058825:0.11274,(t643886010:0.08795,t637000281:0.10708)1.00:0.04396)0.89:0.02581,(t646564572:0.16321,(t643886039:0.11753,t642555160:0.09339)1.00:0.05215)1.00:0.05109)1.00:0.04368)1.00:0.08360)1.00:0.15227)Staphylococcus1.00:0.76048)0.95:0.25974,(t646311941:0.73682,((t647000207:1.06835,((t645951817:0.23965,t647533172:0.24700)1.00:0.39312,t643886188:0.99035)0.97:0.16723)1.00:0.19148,((((t644736382:0.05582,(t639633028:0.01316,t643886139:0.00679)1.00:0.06408)1.00:0.59390,(((t643886217:0.37955,t650377954:0.41989)0.97:0.06199,(t641228495:0.11149,(t650716045:0.08682,t647533176:0.08356)0.94:0.03880)1.00:0.17549)1.00:0.10128,(t648276682:0.48918,t645058712:0.17334)0.46:0.06868)1.00:0.76878)1.00:0.19034,(((t647533194:0.66861,(t639633027:0.48736,t644736381:0.42525)0.25:0.08973)0.25:0.05962,(((t649989969:0.16765,(t638341112:0.21999,t643886050:0.17986)0.95:0.04552)1.00:0.11993,(t647533178:0.31353,t646206276:0.30158)1.00:0.09813)1.00:0.37331,(t643886109:0.17390,(t649633064:0.14957,t641522636:0.17750)1.00:0.12022)1.00:1.02166)1.00:0.11589)1.00:0.10672,(t648276684:0.31905,t643886045:0.37635)1.00:0.29763)0.25:0.08750)Lactobacillus1.00:0.40974,((t650377929:0.26419,(t647533156:0.27068,t647533146:0.27655)0.97:0.07084)1.00:0.22589,(t640069315:0.62191,(((t637000302:0.04157,(t649990016:0.02274,t651053073:0.02748)0.68:0.02378)1.00:0.18880,(t646564575:0.25367,((t638341202:0.22691,(t648276747:0.08769,t650377975:0.04808)1.00:0.18943)1.00:0.08425,(t648276732:0.05642,t641736171:0.06627)1.00:0.12518)0.66:0.04343)0.91:0.04846)1.00:0.08064,(t648276749:0.33677,((((t649990007:0.02984,t649990011:0.06508)1.00:0.03108,(t648028055:0.06246,(t648276734:0.02455,(t649990014:0.01580,t648276739:0.03819)1.00:0.01296)1.00:0.02508)1.00:0.03783)1.00:0.10028,(t650716089:0.09784,t649990003:0.09781)1.00:0.07427)0.99:0.03355,(t649990001:0.18358,(t649990004:0.09027,t640753055:0.12204)0.94:0.04117)0.99:0.04208)1.00:0.10884)0.89:0.05668)Streptococcus1.00:0.45364)1.00:0.54881)0.66:0.10830)1.00:0.15718)1.00:0.40753)1.00:0.23244)1.00:0.79854,(((t646206251:0.54983,t643886110:0.61644)1.00:0.61319,(t643886103:0.68403,(t647000218:0.69258,t649989999:0.37936)1.00:0.66872)1.00:0.62461)0.91:0.23036,(t637000332:1.42246,t646311946:1.12938)1.00:1.33031)0.99:0.33694)1.00:0.63232,(((((t648276710:0.73586,(t649989982:0.48914,t647000289:0.54665)1.00:0.25699)1.00:0.47470,(((t645058761:0.07756,t651324009:0.13259)Anaerococcus1.00:0.32698,(t643886145:0.38805,t643886055:0.32650)1.00:0.17811)1.00:0.89120,(t641380421:1.14288,t648276674:0.87140)0.94:0.24806)1.00:0.23400)1.00:0.47471,t645058705:2.31829)0.95:0.18894,(((t648276712:0.28770,t647000290:0.29998)1.00:0.46439,(t642979371:0.37921,(t640069308:0.28255,t641736113:0.51731)1.00:0.12697)0.97:0.15256)1.00:0.65624,(t637000077:0.63998,t643692016:0.63175)1.00:0.66995)1.00:0.21158)0.49:0.11264,(((t643886181:1.04955,(t650377925:0.74496,(((((t642979369:0.37442,((t640963057:0.22659,(t642791604:0.21513,t640963025:0.26241)1.00:0.09125)1.00:0.13482,(t643886116:0.39599,((t642979359:0.23361,t641736197:0.20069)1.00:0.10447,(t641736133:0.28228,t640963046:0.19463)Dorea0.99:0.06006)1.00:0.09792)0.60:0.04989)Ruminococcus0.86:0.06459)1.00:0.17849,(t643886107:0.54690,(t643886146:0.48773,(t640963024:0.39829,t643886199:0.42881)0.43:0.09687)1.00:0.11526)1.00:0.13359)1.00:0.09840,((t643886104:1.30009,t649989950:0.71542)1.00:0.25959,(t649989922:0.48403,((t641380428:0.19283,t643886112:0.24361)1.00:0.17973,(t648028018:0.22906,t645951835:0.20343)1.00:0.16395)0.99:0.08667)1.00:0.13977)Clostridium1.00:0.19948)0.92:0.05894,(((t645951834:0.70309,(t642979337:0.42615,t644736366:0.44103)1.00:0.20028)0.99:0.14220,((t644736367:0.46986,(t642979356:0.22225,t643886006:0.20446)Roseburia1.00:0.16571)1.00:0.13546,t643886070:1.03339)1.00:0.14903)0.24:0.06889,t640963022:0.79399)0.20:0.05298)1.00:0.08365,(t641380422:0.78877,(t643886203:0.56913,t641736227:0.68083)1.00:0.14367)1.00:0.12104)0.97:0.07985)1.00:0.13824)1.00:0.71173,((((t640963014:1.43820,(t643886206:0.85890,t641736271:0.76972)0.99:0.13558)0.28:0.08445,(t641380427:0.59471,t650377966:0.87211)1.00:0.29480)1.00:0.11825,(t643886143:0.47083,t645951831:0.45539)1.00:0.87717)0.94:0.08006,(t650377938:0.88859,t649633094:0.80911)1.00:0.27472)1.00:0.44590)1.00:0.35200,(t641736193:1.29702,(t649989993:0.77072,:0.52965)1.00:0.66328)Eubacterium1.00:0.33542)0.81:0.11757)1.00:0.26344)1.00:0.17478)0.99:0.22121)0.99:0.22203,(t645951855:0.85506,t647000302:0.62721)1.00:1.79347)0.95:0.12970,(((((((t649989980:0.44052,(t646311928:0.30197,(t643348515:0.29154,((t641736189:0.07804,(t639633010:0.06256,(t642979313:0.02455,t642979312:0.02065)1.00:0.04651)0.89:0.02633)1.00:0.07669,(t642979361:0.16891,(t643886040:0.16533,(t651053005:0.05719,t642555107:0.04800)1.00:0.10646)1.00:0.07163)0.19:0.03981)1.00:0.07782)Bifidobacterium1.00:0.09572)1.00:0.15045)1.00:0.99317,(t648028043:0.79096,(t640963058:0.53569,(t643886015:0.22340,(t649989905:0.02479,t649989901:0.03171)1.00:0.18047)1.00:0.35723)Actinomyces0.62:0.10256)1.00:0.16599)0.99:0.11386,(t644736390:0.52702,(t642555133:0.36312,(t649633093:0.12636,t645058800:0.11675)1.00:0.44380)1.00:0.15632)1.00:0.34427)0.99:0.14775,(t641522641:0.59182,(t642979306:0.44711,((t643692019:0.48635,t647000231:0.38762)0.99:0.08924,(t648276634:0.38218,(t648276633:0.36355,((t643886058:0.09939,(t645058719:0.01224,t643886084:0.01137)1.00:0.06277)1.00:0.09133,(t643692018:0.13765,t643886057:0.14215)1.00:0.06077)1.00:0.21220)1.00:0.11135)1.00:0.15171)0.28:0.06082)Corynebacterium1.00:0.33701)1.00:0.39785)0.71:0.15358,(t651053058:0.52830,t649633084:0.56550)1.00:0.32539)1.00:1.85856,((t645951837:0.55683,(t644736346:0.56842,(t644736358:0.14675,t650377943:0.26040)1.00:0.23770)0.89:0.12932)1.00:0.30101,((t640612206:0.26559,(t642979321:0.12573,t642979320:0.10309)1.00:0.21297)1.00:0.34617,((t644736327:0.24170,t643886019:0.21960)1.00:0.25083,(t648028047:0.31060,t643886063:0.66789)1.00:0.11596)1.00:0.25201)1.00:0.48659)1.00:1.06483)1.00:0.63684,((t640069321:3.07389,(t640753047:1.82952,t637000092:2.64294)0.79:0.17326)0.86:0.17192,((((t637000271:0.90984,((t645058865:0.55603,(t639279312:0.47208,t641522638:0.54130)1.00:0.15964)1.00:0.24275,((t640069327:0.34903,t639633048:0.31147)1.00:0.54194,t648028010:0.94428)0.77:0.10475)1.00:0.17230)1.00:0.67617,((((t643886193:0.21583,(t647533210:0.24836,t649989956:0.19210)0.16:0.04382)1.00:0.11587,(t643886208:0.25511,(t647000283:0.15188,((t643886150:0.02189,t645058748:0.03897)1.00:0.03584,((t643886198:0.02189,t643886194:0.03018)1.00:0.07738,(t643886151:0.03095,(t647000284:0.01736,(t649633075:0.04336,(t641228498:0.02255,t647533186:0.03199)0.80:0.00819)1.00:0.01841)1.00:0.03098)1.00:0.06066)0.97:0.02113)1.00:0.11898)Neisseria1.00:0.12313)0.58:0.04778)1.00:0.82985,(t649990021:1.28919,(t649989970:0.76755,(t641228489:0.68974,(t637000046:0.45744,(t648028033:0.29669,t646206250:0.56508)1.00:0.21135)0.60:0.11121)0.97:0.11702)0.79:0.09869)1.00:0.18159)1.00:0.26088,(t642555169:1.19932,((((t643886024:0.30159,(t640753048:0.19241,(t651053056:0.22624,((t649633041:0.08649,((t643348560:0.00642,t646311937:0.00303)1.00:0.09381,t642979368:0.11613)0.84:0.02239)1.00:0.03586,(((t646862322:0.00605)Escherichia:0.00000,((t641522650:0.02230,t638341196:0.11900)1.00:0.00695,t640427143:0.01101)0.92:0.01075)0.82:0.01536,t643692022:0.03992)1.00:0.07254)1.00:0.12056)0.99:0.06453)1.00:0.09181)1.00:0.26445,((t641736156:0.17684,(t643886008:0.21958,t647533181:0.15327)0.60:0.04229)1.00:0.16278,(t640753001:0.25735,(t637000127:0.22907,((t637000203:0.10224,t647000288:0.09674)1.00:0.10841,((t649989906:0.05089,(t644736324:0.05395,t648028005:0.07584)0.91:0.02238)1.00:0.12402,(t651324039:0.08635,t650377944:0.13190)Haemophilus1.00:0.10250)1.00:0.05068)1.00:0.05656)0.35:0.04382)1.00:0.08047)1.00:0.40025)1.00:0.65600,((t638341158:0.20534,(t637000221:0.14730,t650377963:0.14842)1.00:0.14042)1.00:0.47929,((t646206271:0.10752,((t650377901:0.09491,t646206269:0.10747)1.00:0.06303,(t646206268:0.09860,t646206270:0.10625)1.00:0.05730)0.66:0.03487)Acinetobacter1.00:0.47243,(t646564552:0.49830,(t645951810:0.35249,(t637000226:0.03139,t637000227:0.03298)1.00:0.36282)0.57:0.10347)1.00:0.38615)1.00:0.66564)0.11:0.13932)1.00:0.22480,t645951819:1.42192)0.72:0.10714)0.54:0.14593)1.00:0.92506)1.00:0.75294,((t637000095:0.51681,(t649989917:0.53898,t642979316:0.60272)0.97:0.14948)1.00:1.38324,(t651053029:1.16977,(((t643886009:0.06077,t645058720:0.03647)1.00:0.23775,(t640753010:0.20079,t640753009:0.19765)1.00:0.10310)1.00:0.18727,(t645951857:0.34592,t640753011:0.40921)1.00:0.15998)Campylobacter1.00:0.67270)1.00:1.68116)0.08:0.13022)1.00:0.33470,(((t643886113:0.38687,(t642979305:0.05235,t649989920:0.04871)1.00:0.27483)1.00:0.52426,((t650377904:0.28945,t641736205:0.19327)1.00:0.71790,(t649633078:0.78521,((((t645951840:0.63372,(t648276716:0.30892,(((t649989986:0.19496,t643886200:0.25794)0.98:0.05732,((t648861012:0.07642,t649989989:0.10016)1.00:0.18949,(t645951825:0.33423,((t649989987:0.10015,(t648028051:0.08147,t645951836:0.10696)0.71:0.01992)1.00:0.07452,(t648276715:0.23810,(t648276713:0.17513,t647000292:0.08733)1.00:0.16206)0.99:0.06486)1.00:0.13555)0.99:0.05663)0.16:0.04370)1.00:0.06497,(t649989988:0.19822,(t647000293:0.12894,t647000295:0.14334)1.00:0.17101)0.78:0.04980)1.00:0.08817)1.00:0.26393)Prevotella1.00:0.24393,(((t645058788:0.12426,((t640963023:0.04145,(t642979319:0.05529,(t647000215:0.03155,t651324012:0.01315)1.00:0.02808)1.00:0.01776)0.98:0.01819,t637000026:0.04422)1.00:0.07121)1.00:0.04571,((t643886111:0.03342,t642791621:0.03498)1.00:0.07882,((t649989912:0.03891,t641736196:0.03700)1.00:0.05264,(t641380447:0.06685,t649633012:0.11346)0.99:0.02194)1.00:0.05685)1.00:0.05907)1.00:0.11533,((t642979370:0.00899,t640753008:0.01095)1.00:0.14185,(t643886197:0.11996,(t642979351:0.13831,(t649633013:0.16743,t642791613:0.09293)0.20:0.02952)0.94:0.02920)1.00:0.11861)1.00:0.09617)Bacteroides1.00:0.11562)1.00:0.24050,(t640753039:0.13352,(t640963016:0.03471,t642979358:0.02476)1.00:0.10827)1.00:0.23309)0.99:0.15469,(t642555148:0.39212,(t643886148:0.52057,(t649989985:0.02086,t643886142:0.03850)1.00:0.75598)1.00:0.27610)Porphyromonas1.00:0.27541)1.00:0.35830)0.49:0.16069)1.00:0.60588)1.00:1.04257,(t642555104:1.87557,t650633000:2.10387)0.95:0.37071)0.77:0.31073)0.99:0.21945)1.00:0.23723)0.83:0.13130)0.80:0.16410):1.20714):1.00000; 2 | -------------------------------------------------------------------------------- /data/HMP_tree/tippoint_attr.csv: -------------------------------------------------------------------------------- 1 | ID,Phylum,Type,Size 2 | t637000026,Bacteroidetes,Potential pathogens,312.804878049 3 | t637000046,Proteobacteria,Potential pathogens,60 4 | t637000077,Firmicutes,Potential pathogens,60 5 | t637000092,Thermi,Commensal microbes,20 6 | t637000095,Proteobacteria,Commensal microbes,146.341463415 7 | t637000127,Proteobacteria,Commensal microbes,20 8 | t637000163,Euryarchaeota,Commensal microbes,20 9 | t637000203,Proteobacteria,Potential pathogens,60 10 | t637000221,Proteobacteria,Commensal microbes,25.0000000001 11 | t637000226,Proteobacteria,Commensal microbes,20 12 | t637000227,Proteobacteria,Commensal microbes,20 13 | t637000271,Proteobacteria,Commensal microbes,20 14 | t637000281,Firmicutes,Potential pathogens,450 15 | t637000284,Firmicutes,Potential pathogens,60 16 | t637000302,Firmicutes,Commensal microbes,147.857142857 17 | t637000327,Spirochaetes,Potential pathogens,228.260869565 18 | t637000332,Tenericutes,Potential pathogens,105 19 | t638341112,Firmicutes,Commensal microbes,20 20 | t638341158,Proteobacteria,Potential pathogens,60 21 | t638341196,Proteobacteria,Potential pathogens,60 22 | t638341202,Firmicutes,Potential pathogens,60 23 | t639279312,Proteobacteria,Commensal microbes,20 24 | t639633010,Actinobacteria,Commensal microbes,85.975609756 25 | t639633027,Firmicutes,Commensal microbes,20 26 | t639633028,Firmicutes,Commensal microbes,20 27 | t639633048,Proteobacteria,Commensal microbes,20 28 | t640069308,Firmicutes,Potential pathogens,60 29 | t640069315,Firmicutes,Commensal microbes,60.3658536585 30 | t640069321,Cyanobacteria,Commensal microbes,20 31 | t640069327,Proteobacteria,Commensal microbes,20 32 | t640427121,Euryarchaeota,Commensal microbes,34.7560975609 33 | t640427143,Proteobacteria,Potential pathogens,60 34 | t640612206,Actinobacteria,Commensal microbes,111.585365854 35 | t640753001,Proteobacteria,Commensal microbes,20 36 | t640753008,Bacteroidetes,Potential pathogens,395.12195122 37 | t640753009,Proteobacteria,Potential pathogens,450 38 | t640753010,Proteobacteria,Potential pathogens,332.608695652 39 | t640753011,Proteobacteria,Commensal microbes,25.6097560975 40 | t640753039,Bacteroidetes,Potential pathogens,197.56097561 41 | t640753047,Chloroflexi,Commensal microbes,20 42 | t640753048,Proteobacteria,Potential pathogens,60 43 | t640753055,Firmicutes,Potential pathogens,443.571428571 44 | t640963014,Firmicutes,Potential pathogens,439.024390244 45 | t640963016,Bacteroidetes,Commensal microbes,111.585365854 46 | t640963022,Firmicutes,Commensal microbes,126.219512195 47 | t640963023,Bacteroidetes,Potential pathogens,312.804878049 48 | t640963024,Firmicutes,Commensal microbes,146.341463415 49 | t640963025,Firmicutes,Commensal microbes,148.170731707 50 | t640963046,Firmicutes,Commensal microbes,131.707317073 51 | t640963057,Firmicutes,Commensal microbes,126.219512195 52 | t640963058,Actinobacteria,Potential pathogens,450 53 | t641228489,Proteobacteria,Commensal microbes,20 54 | t641228495,Firmicutes,Commensal microbes,20 55 | t641228498,Proteobacteria,Potential pathogens,397.826086956 56 | t641380421,Firmicutes,Commensal microbes,137.142857143 57 | t641380422,Firmicutes,Commensal microbes,23.7804878049 58 | t641380427,Firmicutes,Commensal microbes,139.024390244 59 | t641380428,Firmicutes,Commensal microbes,95.1219512194 60 | t641380447,Bacteroidetes,Commensal microbes,124.390243902 61 | t641522636,Firmicutes,Commensal microbes,20 62 | t641522638,Proteobacteria,Commensal microbes,20 63 | t641522641,Actinobacteria,Potential pathogens,60 64 | t641522650,Proteobacteria,Potential pathogens,60 65 | t641736113,Firmicutes,Commensal microbes,69.5121951219 66 | t641736133,Firmicutes,Commensal microbes,137.195121951 67 | t641736156,Proteobacteria,Potential pathogens,60 68 | t641736171,Firmicutes,Commensal microbes,20 69 | t641736189,Actinobacteria,Potential pathogens,60 70 | t641736193,Firmicutes,Commensal microbes,20 71 | t641736196,Bacteroidetes,Commensal microbes,98.7804878049 72 | t641736197,Firmicutes,Commensal microbes,85.975609756 73 | t641736205,Bacteroidetes,Potential pathogens,400.609756098 74 | t641736227,Firmicutes,Commensal microbes,45.731707317 75 | t641736271,Firmicutes,Commensal microbes,124.390243902 76 | t642555104,Verrucomicrobia,Commensal microbes,89.6341463415 77 | t642555107,Actinobacteria,Commensal microbes,98.7804878049 78 | t642555133,Actinobacteria,Commensal microbes,20 79 | t642555148,Bacteroidetes,Potential pathogens,60 80 | t642555160,Firmicutes,Potential pathogens,60 81 | t642555169,Proteobacteria,Potential pathogens,60 82 | t642791604,Firmicutes,Commensal microbes,107.926829268 83 | t642791613,Bacteroidetes,Commensal microbes,21.9512195123 84 | t642791621,Bacteroidetes,Commensal microbes,64.0243902439 85 | t642979305,Bacteroidetes,Potential pathogens,450 86 | t642979306,Actinobacteria,Potential pathogens,150 87 | t642979312,Actinobacteria,Commensal microbes,20.1219512195 88 | t642979313,Actinobacteria,Commensal microbes,40.243902439 89 | t642979316,Proteobacteria,Commensal microbes,20 90 | t642979319,Bacteroidetes,Commensal microbes,106.097560976 91 | t642979320,Actinobacteria,Commensal microbes,20 92 | t642979321,Actinobacteria,Commensal microbes,20 93 | t642979351,Bacteroidetes,Commensal microbes,20.1219512195 94 | t642979356,Firmicutes,Commensal microbes,137.195121951 95 | t642979358,Bacteroidetes,Commensal microbes,47.5609756098 96 | t642979359,Firmicutes,Commensal microbes,20 97 | t642979361,Actinobacteria,Commensal microbes,20 98 | t642979367,Firmicutes,Commensal microbes,20 99 | t642979368,Proteobacteria,Potential pathogens,60 100 | t642979369,Firmicutes,Commensal microbes,65.8536585366 101 | t642979370,Bacteroidetes,Commensal microbes,107.926829268 102 | t642979371,Firmicutes,Commensal microbes,20 103 | t643348515,Actinobacteria,Commensal microbes,20 104 | t643348560,Proteobacteria,Potential pathogens,60 105 | t643692016,Firmicutes,Potential pathogens,60 106 | t643692018,Actinobacteria,Potential pathogens,60 107 | t643692019,Actinobacteria,Commensal microbes,20 108 | t643692022,Proteobacteria,Potential pathogens,60 109 | t643886006,Firmicutes,Commensal microbes,137.195121951 110 | t643886008,Proteobacteria,Commensal microbes,45 111 | t643886009,Proteobacteria,Potential pathogens,436.956521739 112 | t643886010,Firmicutes,Commensal microbes,150 113 | t643886015,Actinobacteria,Commensal microbes,143.47826087 114 | t643886019,Actinobacteria,Potential pathogens,276.428571429 115 | t643886024,Proteobacteria,Potential pathogens,60 116 | t643886039,Firmicutes,Commensal microbes,83.3333333334 117 | t643886040,Actinobacteria,Commensal microbes,32.9268292683 118 | t643886045,Firmicutes,Commensal microbes,20 119 | t643886050,Firmicutes,Commensal microbes,60 120 | t643886055,Firmicutes,Commensal microbes,20 121 | t643886057,Actinobacteria,Commensal microbes,20 122 | t643886058,Actinobacteria,Commensal microbes,125 123 | t643886063,Actinobacteria,Commensal microbes,25.0000000001 124 | t643886070,Firmicutes,Commensal microbes,38.5714285714 125 | t643886074,Firmicutes,Commensal microbes,150 126 | t643886084,Actinobacteria,Commensal microbes,116.666666667 127 | t643886103,Firmicutes,Commensal microbes,122.56097561 128 | t643886104,Firmicutes,Commensal microbes,150 129 | t643886107,Firmicutes,Commensal microbes,29.268292683 130 | t643886109,Firmicutes,Commensal microbes,20 131 | t643886110,Firmicutes,Commensal microbes,20 132 | t643886111,Bacteroidetes,Commensal microbes,91.4634146341 133 | t643886112,Firmicutes,Commensal microbes,95.1219512194 134 | t643886113,Bacteroidetes,Potential pathogens,450 135 | t643886116,Firmicutes,Commensal microbes,131.707317073 136 | t643886139,Firmicutes,Commensal microbes,20 137 | t643886142,Bacteroidetes,Commensal microbes,20 138 | t643886143,Firmicutes,Commensal microbes,131.707317073 139 | t643886145,Firmicutes,Commensal microbes,20 140 | t643886146,Firmicutes,Commensal microbes,51.2195121951 141 | t643886148,Bacteroidetes,Commensal microbes,92.1428571429 142 | t643886150,Proteobacteria,Commensal microbes,145.652173913 143 | t643886151,Proteobacteria,Commensal microbes,52.1739130436 144 | t643886181,Firmicutes,Commensal microbes,150 145 | t643886188,Firmicutes,Commensal microbes,139.130434783 146 | t643886193,Proteobacteria,Commensal microbes,150 147 | t643886194,Proteobacteria,Potential pathogens,437.142857143 148 | t643886197,Bacteroidetes,Commensal microbes,20 149 | t643886198,Proteobacteria,Commensal microbes,147.857142857 150 | t643886199,Firmicutes,Commensal microbes,54.8780487806 151 | t643886200,Bacteroidetes,Commensal microbes,29.268292683 152 | t643886203,Firmicutes,Commensal microbes,137.195121951 153 | t643886206,Firmicutes,Commensal microbes,45.731707317 154 | t643886208,Proteobacteria,Potential pathogens,450 155 | t643886217,Firmicutes,Commensal microbes,100 156 | t644736324,Proteobacteria,Commensal microbes,145.652173913 157 | t644736327,Actinobacteria,Commensal microbes,150 158 | t644736346,Actinobacteria,Potential pathogens,60 159 | t644736358,Actinobacteria,Potential pathogens,235.975609756 160 | t644736366,Firmicutes,Commensal microbes,135.365853659 161 | t644736367,Firmicutes,Commensal microbes,146.341463415 162 | t644736381,Firmicutes,Commensal microbes,20 163 | t644736382,Firmicutes,Commensal microbes,20 164 | t644736384,Fusobacteria,Potential pathogens,443.571428571 165 | t644736390,Actinobacteria,Commensal microbes,66.6666666666 166 | t645058705,Firmicutes,Commensal microbes,20 167 | t645058712,Firmicutes,Commensal microbes,34.9999999999 168 | t645058719,Actinobacteria,Commensal microbes,83.3333333334 169 | t645058720,Proteobacteria,Potential pathogens,437.142857143 170 | t645058738,Firmicutes,Commensal microbes,130.714285714 171 | t645058748,Proteobacteria,Potential pathogens,430.434782609 172 | t645058761,Firmicutes,Commensal microbes,20 173 | t645058788,Bacteroidetes,Potential pathogens,214.024390244 174 | t645058800,Actinobacteria,Potential pathogens,450 175 | t645058825,Firmicutes,Commensal microbes,66.6666666666 176 | t645058834,Firmicutes,Potential pathogens,450 177 | t645058865,Proteobacteria,Potential pathogens,60 178 | t645951802,Firmicutes,Commensal microbes,124.285714286 179 | t645951804,Fusobacteria,Commensal microbes,20 180 | t645951808,Firmicutes,Commensal microbes,134.782608696 181 | t645951810,Proteobacteria,Commensal microbes,50 182 | t645951817,Firmicutes,Commensal microbes,150 183 | t645951819,Proteobacteria,Commensal microbes,150 184 | t645951825,Bacteroidetes,Commensal microbes,20 185 | t645951831,Firmicutes,Commensal microbes,146.341463415 186 | t645951833,Firmicutes,Commensal microbes,106.52173913 187 | t645951834,Firmicutes,Commensal microbes,33.3333333333 188 | t645951835,Firmicutes,Commensal microbes,65.8536585366 189 | t645951836,Bacteroidetes,Commensal microbes,145.714285714 190 | t645951837,Actinobacteria,Commensal microbes,42.8571428571 191 | t645951840,Bacteroidetes,Commensal microbes,117.857142857 192 | t645951848,Fusobacteria,Potential pathogens,450 193 | t645951855,Synergistetes,Commensal microbes,20 194 | t645951857,Proteobacteria,Commensal microbes,143.47826087 195 | t645951859,Fusobacteria,Commensal microbes,20 196 | t645951860,Fusobacteria,Commensal microbes,150 197 | t645951869,Spirochaetes,Commensal microbes,105 198 | t646206250,Proteobacteria,Commensal microbes,38.4146341464 199 | t646206251,Firmicutes,Commensal microbes,95.1219512194 200 | t646206254,Fusobacteria,Commensal microbes,20 201 | t646206268,Proteobacteria,Commensal microbes,20 202 | t646206269,Proteobacteria,Potential pathogens,60 203 | t646206270,Proteobacteria,Potential pathogens,60 204 | t646206271,Proteobacteria,Potential pathogens,60 205 | t646206275,Fusobacteria,Commensal microbes,20 206 | t646206276,Firmicutes,Commensal microbes,25.0000000001 207 | t646311901,Firmicutes,Commensal microbes,20 208 | t646311928,Actinobacteria,Potential pathogens,150 209 | t646311937,Proteobacteria,Commensal microbes,20 210 | t646311941,Firmicutes,Potential pathogens,60 211 | t646311946,Tenericutes,Commensal microbes,20 212 | t646311956,Fusobacteria,Potential pathogens,60 213 | t646564552,Proteobacteria,Commensal microbes,33.3333333333 214 | t646564572,Firmicutes,Commensal microbes,20 215 | t646564575,Firmicutes,Potential pathogens,163.043478261 216 | t646862322,Proteobacteria,Potential pathogens,301.829268293 217 | t646862342,Firmicutes,Potential pathogens,125 218 | t647000207,Firmicutes,Commensal microbes,20 219 | t647000215,Bacteroidetes,Commensal microbes,142.682926829 220 | t647000218,Firmicutes,Commensal microbes,25.7142857144 221 | t647000231,Actinobacteria,Potential pathogens,60 222 | t647000254,Fusobacteria,Potential pathogens,450 223 | t647000268,Fusobacteria,Commensal microbes,143.47826087 224 | t647000283,Proteobacteria,Commensal microbes,143.47826087 225 | t647000284,Proteobacteria,Commensal microbes,41.3043478261 226 | t647000288,Proteobacteria,Commensal microbes,20 227 | t647000289,Firmicutes,Commensal microbes,20 228 | t647000290,Firmicutes,Commensal microbes,20 229 | t647000292,Bacteroidetes,Commensal microbes,34.2857142857 230 | t647000293,Bacteroidetes,Commensal microbes,29.268292683 231 | t647000295,Bacteroidetes,Commensal microbes,34.9999999999 232 | t647000302,Synergistetes,Commensal microbes,20 233 | t647000331,Firmicutes,Potential pathogens,450 234 | t647533146,Firmicutes,Potential pathogens,60 235 | t647533156,Firmicutes,Potential pathogens,60 236 | t647533172,Firmicutes,Commensal microbes,145.714285714 237 | t647533176,Firmicutes,Commensal microbes,90 238 | t647533178,Firmicutes,Commensal microbes,20 239 | t647533181,Proteobacteria,Potential pathogens,60 240 | t647533186,Proteobacteria,Potential pathogens,189.130434782 241 | t647533194,Firmicutes,Commensal microbes,20 242 | t647533210,Proteobacteria,Commensal microbes,47.1428571429 243 | t648028005,Proteobacteria,Potential pathogens,293.478260869 244 | t648028010,Proteobacteria,Commensal microbes,20 245 | t648028018,Firmicutes,Commensal microbes,20 246 | t648028033,Proteobacteria,Commensal microbes,20 247 | t648028043,Actinobacteria,Commensal microbes,20 248 | t648028047,Actinobacteria,Commensal microbes,20 249 | t648028051,Bacteroidetes,Commensal microbes,150 250 | t648028055,Firmicutes,Potential pathogens,335.714285714 251 | t648276633,Actinobacteria,Commensal microbes,33.3333333333 252 | t648276634,Actinobacteria,Potential pathogens,450 253 | t648276674,Firmicutes,Commensal microbes,58.3333333333 254 | t648276682,Firmicutes,Commensal microbes,60 255 | t648276684,Firmicutes,Commensal microbes,20 256 | t648276710,Firmicutes,Commensal microbes,20 257 | t648276712,Firmicutes,Commensal microbes,141.428571429 258 | t648276713,Bacteroidetes,Commensal microbes,34.2857142857 259 | t648276715,Bacteroidetes,Commensal microbes,143.571428571 260 | t648276716,Bacteroidetes,Commensal microbes,60.8695652174 261 | t648276732,Firmicutes,Commensal microbes,20 262 | t648276734,Firmicutes,Potential pathogens,450 263 | t648276739,Firmicutes,Commensal microbes,150 264 | t648276747,Firmicutes,Potential pathogens,60 265 | t648276749,Firmicutes,Potential pathogens,60 266 | t648276753,Firmicutes,Commensal microbes,150 267 | t648861012,Bacteroidetes,Commensal microbes,145.714285714 268 | t649633012,Bacteroidetes,Commensal microbes,20 269 | t649633013,Bacteroidetes,Commensal microbes,20 270 | t649633041,Proteobacteria,Commensal microbes,20 271 | t649633064,Firmicutes,Commensal microbes,20 272 | t649633075,Proteobacteria,Commensal microbes,23.9130434782 273 | t649633078,Bacteroidetes,Commensal microbes,111.585365854 274 | t649633084,Actinobacteria,Commensal microbes,20 275 | t649633093,Actinobacteria,Commensal microbes,150 276 | t649633094,Firmicutes,Commensal microbes,102.43902439 277 | t649989901,Actinobacteria,Commensal microbes,150 278 | t649989905,Actinobacteria,Potential pathogens,450 279 | t649989906,Proteobacteria,Commensal microbes,145.652173913 280 | t649989912,Bacteroidetes,Commensal microbes,69.5121951219 281 | t649989917,Proteobacteria,Commensal microbes,115.243902439 282 | t649989920,Bacteroidetes,Potential pathogens,450 283 | t649989922,Firmicutes,Commensal microbes,60.3658536585 284 | t649989928,Firmicutes,Commensal microbes,32.1428571429 285 | t649989950,Firmicutes,Commensal microbes,150 286 | t649989952,Firmicutes,Potential pathogens,450 287 | t649989956,Proteobacteria,Commensal microbes,119.565217391 288 | t649989969,Firmicutes,Commensal microbes,20 289 | t649989970,Proteobacteria,Commensal microbes,147.826086957 290 | t649989971,Firmicutes,Commensal microbes,143.571428571 291 | t649989980,Actinobacteria,Commensal microbes,20 292 | t649989982,Firmicutes,Commensal microbes,33.3333333333 293 | t649989985,Bacteroidetes,Commensal microbes,25.6097560975 294 | t649989986,Bacteroidetes,Commensal microbes,36.9565217391 295 | t649989987,Bacteroidetes,Commensal microbes,137.142857143 296 | t649989988,Bacteroidetes,Commensal microbes,50 297 | t649989989,Bacteroidetes,Commensal microbes,150 298 | t649989993,Firmicutes,Commensal microbes,20 299 | t649989996,Firmicutes,Commensal microbes,117.391304348 300 | t649989999,Firmicutes,Commensal microbes,150 301 | t649990001,Firmicutes,Commensal microbes,143.47826087 302 | t649990003,Firmicutes,Commensal microbes,150 303 | t649990004,Firmicutes,Commensal microbes,147.826086957 304 | t649990007,Firmicutes,Commensal microbes,150 305 | t649990011,Firmicutes,Commensal microbes,150 306 | t649990014,Firmicutes,Potential pathogens,450 307 | t649990016,Firmicutes,Commensal microbes,150 308 | t649990021,Proteobacteria,Commensal microbes,51.2195121951 309 | t649990026,Spirochaetes,Commensal microbes,20 310 | t650377901,Proteobacteria,Potential pathogens,60 311 | t650377904,Bacteroidetes,Commensal microbes,137.195121951 312 | t650377925,Firmicutes,Commensal microbes,104.268292683 313 | t650377929,Firmicutes,Potential pathogens,60 314 | t650377938,Firmicutes,Commensal microbes,93.2926829268 315 | t650377943,Actinobacteria,Commensal microbes,87.8048780489 316 | t650377944,Proteobacteria,Potential pathogens,450 317 | t650377954,Firmicutes,Commensal microbes,20 318 | t650377958,Firmicutes,Commensal microbes,20 319 | t650377963,Proteobacteria,Commensal microbes,20 320 | t650377966,Firmicutes,Commensal microbes,96.9512195122 321 | t650377974,Firmicutes,Commensal microbes,20 322 | t650377975,Firmicutes,Potential pathogens,60 323 | t650633000,Lentisphaerae,Commensal microbes,40.243902439 324 | t650716045,Firmicutes,Commensal microbes,20 325 | t650716089,Firmicutes,Commensal microbes,150 326 | t651053005,Actinobacteria,Commensal microbes,20 327 | t651053029,Proteobacteria,Potential pathogens,60 328 | t651053056,Proteobacteria,Potential pathogens,60 329 | t651053058,Actinobacteria,Potential pathogens,450 330 | t651053073,Firmicutes,Commensal microbes,150 331 | t651324009,Firmicutes,Commensal microbes,20 332 | t651324012,Bacteroidetes,Commensal microbes,137.195121951 333 | t651324039,Proteobacteria,Commensal microbes,150 334 | -------------------------------------------------------------------------------- /data/Methanotroph/metadata.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/plotting-tree-with-data-using-ggtreeExtra/4e089aa5caea12c3e6110e07dbb257c7b6e25214/data/Methanotroph/metadata.csv -------------------------------------------------------------------------------- /data/PhyloPhlAn/ringpoint_attr.csv: -------------------------------------------------------------------------------- 1 | ID,Pos,Type 2 | t2507262051,0.35,Mislabelled 3 | t2509887034,0.35,Mislabelled 4 | t2509276051,0.35,Mislabelled 5 | t637000012,0.35,Mislabelled 6 | t637000019,0.35,Mislabelled 7 | t637000020,0.35,Mislabelled 8 | t650716010,0.35,Mislabelled 9 | t637000058,0.35,Mislabelled 10 | t637000137,0.35,Mislabelled 11 | t637000160,0.35,Mislabelled 12 | t637000201,0.35,Mislabelled 13 | t637000309,0.35,Mislabelled 14 | t637000310,0.35,Mislabelled 15 | t637000311,0.35,Mislabelled 16 | t637000312,0.35,Mislabelled 17 | t637000313,0.35,Mislabelled 18 | t637000314,0.35,Mislabelled 19 | t650716053,0.35,Mislabelled 20 | t650716066,0.35,Mislabelled 21 | t638341009,0.35,Mislabelled 22 | t638341014,0.35,Mislabelled 23 | t638341056,0.35,Mislabelled 24 | t638341059,0.35,Mislabelled 25 | t638341070,0.35,Mislabelled 26 | t638341093,0.35,Mislabelled 27 | t638341107,0.35,Mislabelled 28 | t638341124,0.35,Mislabelled 29 | t638341141,0.35,Mislabelled 30 | t638341142,0.35,Mislabelled 31 | t638341167,0.35,Mislabelled 32 | t641380428,0.35,Mislabelled 33 | t638341213,0.35,Mislabelled 34 | t638341214,0.35,Mislabelled 35 | t638341215,0.35,Mislabelled 36 | t641380442,0.35,Mislabelled 37 | t638341246,0.35,Mislabelled 38 | t638341247,0.35,Mislabelled 39 | t639633007,0.35,Mislabelled 40 | t639633019,0.35,Mislabelled 41 | t639633036,0.35,Mislabelled 42 | t639633046,0.35,Mislabelled 43 | t651324076,0.35,Mislabelled 44 | t639857006,0.35,Mislabelled 45 | t639857007,0.35,Mislabelled 46 | t639857020,0.35,Mislabelled 47 | t639857034,0.35,Mislabelled 48 | t647000330,0.35,Mislabelled 49 | t639857036,0.35,Mislabelled 50 | t640069309,0.35,Mislabelled 51 | t640427107,0.35,Mislabelled 52 | t640427148,0.35,Mislabelled 53 | t640427149,0.35,Mislabelled 54 | t640427153,0.35,Mislabelled 55 | t640612200,0.35,Mislabelled 56 | t640612202,0.35,Mislabelled 57 | t640612203,0.35,Mislabelled 58 | t640753033,0.35,Mislabelled 59 | t640753037,0.35,Mislabelled 60 | t640753056,0.35,Mislabelled 61 | t640963002,0.35,Mislabelled 62 | t640963011,0.35,Mislabelled 63 | t640963012,0.35,Mislabelled 64 | t640963026,0.35,Mislabelled 65 | t640963028,0.35,Mislabelled 66 | t643348528,0.35,Mislabelled 67 | t640963033,0.35,Mislabelled 68 | t640963037,0.35,Mislabelled 69 | t647533236,0.35,Mislabelled 70 | t641228486,0.35,Mislabelled 71 | t641380427,0.35,Mislabelled 72 | t643692051,0.35,Mislabelled 73 | t641380439,0.35,Mislabelled 74 | t641380440,0.35,Mislabelled 75 | t641380441,0.35,Mislabelled 76 | t643886056,0.35,Mislabelled 77 | t641380446,0.35,Mislabelled 78 | t641380448,0.35,Mislabelled 79 | t641522626,0.35,Mislabelled 80 | t641522654,0.35,Mislabelled 81 | t643886206,0.35,Mislabelled 82 | t641736109,0.35,Mislabelled 83 | t641736156,0.35,Mislabelled 84 | t641736169,0.35,Mislabelled 85 | t641736192,0.35,Mislabelled 86 | t641736197,0.35,Mislabelled 87 | t641736198,0.35,Mislabelled 88 | t641736270,0.35,Mislabelled 89 | t641736270,0.5,Mislabelled 90 | t650716011,0.35,Mislabelled 91 | t650716015,0.35,Mislabelled 92 | t645058869,0.35,Mislabelled 93 | t642555115,0.35,Mislabelled 94 | t642555132,0.35,Mislabelled 95 | t642555138,0.35,Mislabelled 96 | t649633010,0.35,Mislabelled 97 | t649633045,0.35,Mislabelled 98 | t642791610,0.35,Mislabelled 99 | t642791618,0.35,Mislabelled 100 | t642791634,0.35,Mislabelled 101 | t642979359,0.35,Mislabelled 102 | t642979360,0.35,Mislabelled 103 | t642979369,0.35,Mislabelled 104 | t649989911,0.35,Mislabelled 105 | t643348524,0.35,Mislabelled 106 | t651053077,0.35,Mislabelled 107 | t651285002,0.35,Mislabelled 108 | t643348556,0.35,Mislabelled 109 | t643348585,0.35,Mislabelled 110 | t649989923,0.35,Mislabelled 111 | t643692023,0.35,Mislabelled 112 | t646311912,0.35,Mislabelled 113 | t649989945,0.35,Mislabelled 114 | t643886005,0.35,Mislabelled 115 | t649989957,0.35,Mislabelled 116 | t646564511,0.35,Mislabelled 117 | t643886079,0.35,Mislabelled 118 | t643886097,0.35,Mislabelled 119 | t643886112,0.35,Mislabelled 120 | t643886118,0.35,Mislabelled 121 | t647533251,0.35,Mislabelled 122 | t644736396,0.35,Mislabelled 123 | t644736410,0.35,Mislabelled 124 | t650377969,0.35,Mislabelled 125 | t650377973,0.35,Mislabelled 126 | t645058753,0.35,Mislabelled 127 | t645058763,0.35,Mislabelled 128 | t648276721,0.35,Mislabelled 129 | t650716067,0.35,Mislabelled 130 | t651324099,0.35,Mislabelled 131 | t651324107,0.35,Mislabelled 132 | t651324112,0.35,Mislabelled 133 | t645058870,0.35,Mislabelled 134 | t650716027,0.35,Mislabelled 135 | t648861011,0.35,Mislabelled 136 | t645951824,0.35,Mislabelled 137 | t645951835,0.35,Mislabelled 138 | t646206251,0.35,Mislabelled 139 | t650716052,0.35,Mislabelled 140 | t649633052,0.35,Mislabelled 141 | t647000294,0.35,Mislabelled 142 | t646564509,0.35,Mislabelled 143 | t646206260,0.35,Mislabelled 144 | t650716094,0.35,Mislabelled 145 | t651053076,0.35,Mislabelled 146 | t647533200,0.35,Mislabelled 147 | t646564585,0.35,Mislabelled 148 | t647533202,0.35,Mislabelled 149 | t649989921,0.35,Mislabelled 150 | t646311907,0.35,Mislabelled 151 | t646311908,0.35,Mislabelled 152 | t647533238,0.35,Mislabelled 153 | t649989926,0.35,Mislabelled 154 | t647533248,0.35,Mislabelled 155 | t648276673,0.35,Mislabelled 156 | t647533246,0.35,Mislabelled 157 | t647533247,0.35,Mislabelled 158 | t651324055,0.35,Mislabelled 159 | t646564584,0.35,Mislabelled 160 | t651324113,0.35,Mislabelled 161 | t649990023,0.35,Mislabelled 162 | t647000286,0.35,Mislabelled 163 | t648028018,0.35,Mislabelled 164 | t648276601,0.35,Mislabelled 165 | t647000261,0.35,Mislabelled 166 | t648276759,0.35,Mislabelled 167 | t647533197,0.35,Mislabelled 168 | t647533198,0.35,Mislabelled 169 | t649633076,0.35,Mislabelled 170 | t651324114,0.35,Mislabelled 171 | t651324052,0.35,Mislabelled 172 | t647533122,0.35,Mislabelled 173 | t647533249,0.35,Mislabelled 174 | t647533157,0.35,Mislabelled 175 | t650716044,0.35,Mislabelled 176 | t651324048,0.35,Mislabelled 177 | t650716040,0.35,Mislabelled 178 | t651324081,0.35,Mislabelled 179 | t647533191,0.35,Mislabelled 180 | t650716020,0.35,Mislabelled 181 | t649989983,0.35,Mislabelled 182 | t649989922,0.35,Mislabelled 183 | t647533250,0.35,Mislabelled 184 | t649989924,0.35,Mislabelled 185 | t650377923,0.35,Mislabelled 186 | t650716078,0.35,Mislabelled 187 | t647533237,0.35,Mislabelled 188 | t650716017,0.35,Mislabelled 189 | t649989909,0.35,Mislabelled 190 | t651324051,0.35,Mislabelled 191 | t650377924,0.35,Mislabelled 192 | t650377935,0.35,Mislabelled 193 | t649990022,0.35,Mislabelled 194 | t650716043,0.35,Mislabelled 195 | t651324024,0.35,Mislabelled 196 | t649633002,0.35,Mislabelled 197 | t648276617,0.35,Mislabelled 198 | t648861001,0.5,Corrections 199 | t643348513,0.5,Corrections 200 | t641736270,0.5,Corrections 201 | t641522661,0.5,Corrections 202 | t646311937,0.5,Corrections 203 | t637000315,0.5,Corrections 204 | t641736270,0.35,Corrections 205 | t645058746,0.5,Corrections 206 | t649989958,0.5,Corrections 207 | t651324049,0.5,Corrections 208 | t651324050,0.5,Corrections 209 | t651324046,0.5,Corrections 210 | t643348534,0.5,Corrections 211 | t647533126,0.5,Corrections 212 | t642555168,0.5,Corrections 213 | t639857003,0.5,Corrections 214 | t647000238,0.5,Corrections 215 | t651324077,0.5,Corrections 216 | t651324038,0.5,Corrections 217 | t647533243,0.5,Corrections 218 | t645058782,0.5,Corrections 219 | t639857035,0.5,Corrections 220 | t645058835,0.5,Corrections 221 | t648861002,0.5,Corrections 222 | t640963029,0.5,Corrections 223 | t647533112,0.5,Corrections 224 | t651324053,0.5,Corrections 225 | t2500069000,0.35,Insertions 226 | t2501416923,0.35,Insertions 227 | t2501416924,0.35,Insertions 228 | t2501416926,0.35,Insertions 229 | t2501533205,0.35,Insertions 230 | t2501915963,0.35,Insertions 231 | t2501939620,0.35,Insertions 232 | t2502422321,0.35,Insertions 233 | t2502545039,0.35,Insertions 234 | t2502790015,0.35,Insertions 235 | t2503113005,0.35,Insertions 236 | t2503198000,0.35,Insertions 237 | t2503283010,0.35,Insertions 238 | t2503386004,0.35,Insertions 239 | t2503508007,0.35,Insertions 240 | t2503508009,0.35,Insertions 241 | t2503538010,0.35,Insertions 242 | t2503538017,0.35,Insertions 243 | t2503538034,0.35,Insertions 244 | t2503692001,0.35,Insertions 245 | t2503707007,0.35,Insertions 246 | t2503754046,0.35,Insertions 247 | t2503904012,0.35,Insertions 248 | t2503982034,0.35,Insertions 249 | t2503982039,0.35,Insertions 250 | t2503982046,0.35,Insertions 251 | t2504136000,0.35,Insertions 252 | t2504136006,0.35,Insertions 253 | t2504136008,0.35,Insertions 254 | t2504136012,0.35,Insertions 255 | t2504557006,0.35,Insertions 256 | t2504557012,0.35,Insertions 257 | t2504643006,0.35,Insertions 258 | t2504643024,0.35,Insertions 259 | t2504756004,0.35,Insertions 260 | t2504756006,0.35,Insertions 261 | t2504756018,0.35,Insertions 262 | t2504756052,0.35,Insertions 263 | t2504756058,0.35,Insertions 264 | t2505119042,0.35,Insertions 265 | t2505119043,0.35,Insertions 266 | t2505313033,0.35,Insertions 267 | t2505313034,0.35,Insertions 268 | t2505313035,0.35,Insertions 269 | t2505313036,0.35,Insertions 270 | t2505313037,0.35,Insertions 271 | t2505313038,0.35,Insertions 272 | t2505313039,0.35,Insertions 273 | t2505313066,0.35,Insertions 274 | t2505313067,0.35,Insertions 275 | t2505313068,0.35,Insertions 276 | t2505313069,0.35,Insertions 277 | t2505313070,0.35,Insertions 278 | t2505313071,0.35,Insertions 279 | t2505313072,0.35,Insertions 280 | t2505679006,0.35,Insertions 281 | t2505679007,0.35,Insertions 282 | t2505679008,0.35,Insertions 283 | t2505679009,0.35,Insertions 284 | t2505679016,0.35,Insertions 285 | t2505679018,0.35,Insertions 286 | t2505679024,0.35,Insertions 287 | t2505679030,0.35,Insertions 288 | t2505679031,0.35,Insertions 289 | t2505679034,0.35,Insertions 290 | t2505679045,0.35,Insertions 291 | t2505679068,0.35,Insertions 292 | t2505679076,0.35,Insertions 293 | t2505679077,0.35,Insertions 294 | t2505679078,0.35,Insertions 295 | t2505679080,0.35,Insertions 296 | t2505679082,0.35,Insertions 297 | t2506210002,0.35,Insertions 298 | t2506210003,0.35,Insertions 299 | t2506210005,0.35,Insertions 300 | t2506381019,0.35,Insertions 301 | t2506381020,0.35,Insertions 302 | t2506381022,0.35,Insertions 303 | t2506381023,0.35,Insertions 304 | t2506381024,0.35,Insertions 305 | t2506485001,0.35,Insertions 306 | t2506520007,0.35,Insertions 307 | t2506520013,0.35,Insertions 308 | t2506520015,0.35,Insertions 309 | t2506520016,0.35,Insertions 310 | t2506520020,0.35,Insertions 311 | t2506520035,0.35,Insertions 312 | t2506520037,0.35,Insertions 313 | t2506520038,0.35,Insertions 314 | t2506520040,0.35,Insertions 315 | t2506520041,0.35,Insertions 316 | t2506520042,0.35,Insertions 317 | t2506520043,0.35,Insertions 318 | t2506520045,0.35,Insertions 319 | t2506520046,0.35,Insertions 320 | t2506520047,0.35,Insertions 321 | t2506520049,0.35,Insertions 322 | t2506520050,0.35,Insertions 323 | t2506783006,0.35,Insertions 324 | t2506783008,0.35,Insertions 325 | t2506783010,0.35,Insertions 326 | t2506783011,0.35,Insertions 327 | t2506783014,0.35,Insertions 328 | t2506783038,0.35,Insertions 329 | t2506783044,0.35,Insertions 330 | t2506783045,0.35,Insertions 331 | t2506783046,0.35,Insertions 332 | t2506783048,0.35,Insertions 333 | t2506783053,0.35,Insertions 334 | t2506783059,0.35,Insertions 335 | t2506783060,0.35,Insertions 336 | t2506783061,0.35,Insertions 337 | t2506783062,0.35,Insertions 338 | t2506783063,0.35,Insertions 339 | t2506783064,0.35,Insertions 340 | t2506783065,0.35,Insertions 341 | t2507149014,0.35,Insertions 342 | t2507149015,0.35,Insertions 343 | t2507149019,0.35,Insertions 344 | t2507149024,0.35,Insertions 345 | t2507262005,0.35,Insertions 346 | t2507262015,0.35,Insertions 347 | t2507262026,0.35,Insertions 348 | t2507262027,0.35,Insertions 349 | t2507262030,0.35,Insertions 350 | t2507262031,0.35,Insertions 351 | t2507262035,0.35,Insertions 352 | t2507262036,0.35,Insertions 353 | t2507262044,0.35,Insertions 354 | t2507262045,0.35,Insertions 355 | t2507262046,0.35,Insertions 356 | t2507262047,0.35,Insertions 357 | t2510065045,0.35,Insertions 358 | t2507262051,0.35,Insertions 359 | t2507262052,0.35,Insertions 360 | t2507262054,0.35,Insertions 361 | t2507262055,0.35,Insertions 362 | t2507525000,0.35,Insertions 363 | t2507525018,0.35,Insertions 364 | t2508501001,0.35,Insertions 365 | t2508501002,0.35,Insertions 366 | t2508501004,0.35,Insertions 367 | t2508501009,0.35,Insertions 368 | t2508501010,0.35,Insertions 369 | t2508501012,0.35,Insertions 370 | t2508501013,0.35,Insertions 371 | t2508501021,0.35,Insertions 372 | t2508501023,0.35,Insertions 373 | t2508501038,0.35,Insertions 374 | t2508501039,0.35,Insertions 375 | t2508501040,0.35,Insertions 376 | t2508501042,0.35,Insertions 377 | t2508501043,0.35,Insertions 378 | t2508501044,0.35,Insertions 379 | t2508501045,0.35,Insertions 380 | t2508501046,0.35,Insertions 381 | t2508501047,0.35,Insertions 382 | t2508501048,0.35,Insertions 383 | t2508501050,0.35,Insertions 384 | t2508501051,0.35,Insertions 385 | t2508501052,0.35,Insertions 386 | t2508501066,0.35,Insertions 387 | t2508501067,0.35,Insertions 388 | t2508501068,0.35,Insertions 389 | t2508501069,0.35,Insertions 390 | t2508501070,0.35,Insertions 391 | t2508501071,0.35,Insertions 392 | t2508501098,0.35,Insertions 393 | t2508501100,0.35,Insertions 394 | t2508501103,0.35,Insertions 395 | t2508501106,0.35,Insertions 396 | t2508501107,0.35,Insertions 397 | t2508501108,0.35,Insertions 398 | t2508501110,0.35,Insertions 399 | t2508501111,0.35,Insertions 400 | t2508501114,0.35,Insertions 401 | t2508501115,0.35,Insertions 402 | t2508501116,0.35,Insertions 403 | t2508501117,0.35,Insertions 404 | t2508501119,0.35,Insertions 405 | t2508501120,0.35,Insertions 406 | t2508501122,0.35,Insertions 407 | t2508501123,0.35,Insertions 408 | t2508501124,0.35,Insertions 409 | t2508501125,0.35,Insertions 410 | t2508501126,0.35,Insertions 411 | t2508501127,0.35,Insertions 412 | t2508501128,0.35,Insertions 413 | t2508501136,0.35,Insertions 414 | t2509276000,0.35,Insertions 415 | t2509276001,0.35,Insertions 416 | t2509276002,0.35,Insertions 417 | t2509276007,0.35,Insertions 418 | t2509276008,0.35,Insertions 419 | t2509276018,0.35,Insertions 420 | t2509276019,0.35,Insertions 421 | t2509276020,0.35,Insertions 422 | t2509276021,0.35,Insertions 423 | t2509276022,0.35,Insertions 424 | t2509276023,0.35,Insertions 425 | t2509276025,0.35,Insertions 426 | t2509276026,0.35,Insertions 427 | t2509276029,0.35,Insertions 428 | t2509276033,0.35,Insertions 429 | t2509276034,0.35,Insertions 430 | t2509276035,0.35,Insertions 431 | t2509276036,0.35,Insertions 432 | t2509276044,0.35,Insertions 433 | t2509276048,0.35,Insertions 434 | t2509276051,0.35,Insertions 435 | t2511231095,0.35,Insertions 436 | t2509276052,0.35,Insertions 437 | t2509276054,0.35,Insertions 438 | t2509276055,0.35,Insertions 439 | t2509276057,0.35,Insertions 440 | t2509276058,0.35,Insertions 441 | t2509276059,0.35,Insertions 442 | t2509276062,0.35,Insertions 443 | t2509276063,0.35,Insertions 444 | t2509276064,0.35,Insertions 445 | t2509276065,0.35,Insertions 446 | t2509276066,0.35,Insertions 447 | t2509276067,0.35,Insertions 448 | t2509601001,0.35,Insertions 449 | t2509601004,0.35,Insertions 450 | t2509601011,0.35,Insertions 451 | t2509601014,0.35,Insertions 452 | t2509601017,0.35,Insertions 453 | t2509601019,0.35,Insertions 454 | t2509601020,0.35,Insertions 455 | t2509601028,0.35,Insertions 456 | t2509601029,0.35,Insertions 457 | t2509601034,0.35,Insertions 458 | t2509601035,0.35,Insertions 459 | t2509601036,0.35,Insertions 460 | t2509601038,0.35,Insertions 461 | t2509601041,0.35,Insertions 462 | t2509601042,0.35,Insertions 463 | t2509601044,0.35,Insertions 464 | t2509601047,0.35,Insertions 465 | t2509887025,0.35,Insertions 466 | t2509887032,0.35,Insertions 467 | t2509887033,0.35,Insertions 468 | t2511231131,0.35,Insertions 469 | t2509887034,0.35,Insertions 470 | t2510065010,0.35,Insertions 471 | t2510065015,0.35,Insertions 472 | t2510065016,0.35,Insertions 473 | t2510065019,0.35,Insertions 474 | t2510065021,0.35,Insertions 475 | t2510065031,0.35,Insertions 476 | t2510065032,0.35,Insertions 477 | t2510065044,0.35,Insertions 478 | t2511231141,0.35,Insertions 479 | t2510065046,0.35,Insertions 480 | t2510065049,0.35,Insertions 481 | t2510065050,0.35,Insertions 482 | t2510065052,0.35,Insertions 483 | t2510065056,0.35,Insertions 484 | t2510065057,0.35,Insertions 485 | t2510065059,0.35,Insertions 486 | t2510065060,0.35,Insertions 487 | t2510065062,0.35,Insertions 488 | t2510065076,0.35,Insertions 489 | t2510065083,0.35,Insertions 490 | t2510065084,0.35,Insertions 491 | t2510065085,0.35,Insertions 492 | t2510065086,0.35,Insertions 493 | t2510065087,0.35,Insertions 494 | t2510065088,0.35,Insertions 495 | t2510436001,0.35,Insertions 496 | t2510436004,0.35,Insertions 497 | t2510436005,0.35,Insertions 498 | t2510461000,0.35,Insertions 499 | t2510461043,0.35,Insertions 500 | t2510461053,0.35,Insertions 501 | t2510461070,0.35,Insertions 502 | t2510461076,0.35,Insertions 503 | t2510917000,0.35,Insertions 504 | t2510917010,0.35,Insertions 505 | t2510917032,0.35,Insertions 506 | t2510917033,0.35,Insertions 507 | t2510917034,0.35,Insertions 508 | t2510917035,0.35,Insertions 509 | t2510917036,0.35,Insertions 510 | t2510917037,0.35,Insertions 511 | t2511231030,0.35,Insertions 512 | t2511231037,0.35,Insertions 513 | t2511231038,0.35,Insertions 514 | t2511231045,0.35,Insertions 515 | t2511231049,0.35,Insertions 516 | t2511231052,0.35,Insertions 517 | t2511231054,0.35,Insertions 518 | t2511231055,0.35,Insertions 519 | t2511231056,0.35,Insertions 520 | t2511231057,0.35,Insertions 521 | t2511231058,0.35,Insertions 522 | t2511231059,0.35,Insertions 523 | t2511231060,0.35,Insertions 524 | t2511231061,0.35,Insertions 525 | t2511231062,0.35,Insertions 526 | t2511231063,0.35,Insertions 527 | t2511231064,0.35,Insertions 528 | t2511231065,0.35,Insertions 529 | t2511231066,0.35,Insertions 530 | t2511231067,0.35,Insertions 531 | t2511231069,0.35,Insertions 532 | t2511231070,0.35,Insertions 533 | t2511231071,0.35,Insertions 534 | t2511231072,0.35,Insertions 535 | t2511231073,0.35,Insertions 536 | t2511231074,0.35,Insertions 537 | t2511231075,0.35,Insertions 538 | t2511231076,0.35,Insertions 539 | t2511231077,0.35,Insertions 540 | t2511231078,0.35,Insertions 541 | t2511231079,0.35,Insertions 542 | t2511231080,0.35,Insertions 543 | t2511231081,0.35,Insertions 544 | t2511231082,0.35,Insertions 545 | t2511231083,0.35,Insertions 546 | t2511231084,0.35,Insertions 547 | t2511231085,0.35,Insertions 548 | t2511231086,0.35,Insertions 549 | t2511231087,0.35,Insertions 550 | t2511231088,0.35,Insertions 551 | t2511231089,0.35,Insertions 552 | t2511231090,0.35,Insertions 553 | t2511231091,0.35,Insertions 554 | t2511231092,0.35,Insertions 555 | t2511231094,0.35,Insertions 556 | t2511231221,0.35,Insertions 557 | t2511231097,0.35,Insertions 558 | t2511231098,0.35,Insertions 559 | t2511231099,0.35,Insertions 560 | t2511231100,0.35,Insertions 561 | t2511231101,0.35,Insertions 562 | t2511231102,0.35,Insertions 563 | t2511231103,0.35,Insertions 564 | t2511231104,0.35,Insertions 565 | t2511231105,0.35,Insertions 566 | t2511231106,0.35,Insertions 567 | t2511231107,0.35,Insertions 568 | t2511231108,0.35,Insertions 569 | t2511231110,0.35,Insertions 570 | t2511231111,0.35,Insertions 571 | t2511231112,0.35,Insertions 572 | t2511231113,0.35,Insertions 573 | t2511231114,0.35,Insertions 574 | t2511231115,0.35,Insertions 575 | t2511231116,0.35,Insertions 576 | t2511231118,0.35,Insertions 577 | t2511231119,0.35,Insertions 578 | t2511231120,0.35,Insertions 579 | t2511231121,0.35,Insertions 580 | t2511231122,0.35,Insertions 581 | t2511231123,0.35,Insertions 582 | t2511231124,0.35,Insertions 583 | t2511231125,0.35,Insertions 584 | t2511231126,0.35,Insertions 585 | t2511231127,0.35,Insertions 586 | t2511231128,0.35,Insertions 587 | t2511231129,0.35,Insertions 588 | t2511231130,0.35,Insertions 589 | t2512047071,0.35,Insertions 590 | t2511231132,0.35,Insertions 591 | t2511231133,0.35,Insertions 592 | t2511231134,0.35,Insertions 593 | t2511231135,0.35,Insertions 594 | t2511231136,0.35,Insertions 595 | t2511231137,0.35,Insertions 596 | t2511231138,0.35,Insertions 597 | t2511231139,0.35,Insertions 598 | t2511231140,0.35,Insertions 599 | t2512047081,0.35,Insertions 600 | t2511231142,0.35,Insertions 601 | t2511231143,0.35,Insertions 602 | t2511231144,0.35,Insertions 603 | t2511231145,0.35,Insertions 604 | t2511231146,0.35,Insertions 605 | t2511231147,0.35,Insertions 606 | t2511231149,0.35,Insertions 607 | t2511231150,0.35,Insertions 608 | t2511231151,0.35,Insertions 609 | t2511231152,0.35,Insertions 610 | t2511231153,0.35,Insertions 611 | t2511231154,0.35,Insertions 612 | t2511231155,0.35,Insertions 613 | t2511231156,0.35,Insertions 614 | t2511231157,0.35,Insertions 615 | t2511231158,0.35,Insertions 616 | t2511231159,0.35,Insertions 617 | t2511231160,0.35,Insertions 618 | t2511231161,0.35,Insertions 619 | t2511231162,0.35,Insertions 620 | t2511231163,0.35,Insertions 621 | t2511231164,0.35,Insertions 622 | t2511231165,0.35,Insertions 623 | t2511231166,0.35,Insertions 624 | t2511231167,0.35,Insertions 625 | t2511231168,0.35,Insertions 626 | t2511231169,0.35,Insertions 627 | t2511231170,0.35,Insertions 628 | t2511231171,0.35,Insertions 629 | t2511231172,0.35,Insertions 630 | t2511231173,0.35,Insertions 631 | t2511231174,0.35,Insertions 632 | t2511231175,0.35,Insertions 633 | t2511231176,0.35,Insertions 634 | t2511231177,0.35,Insertions 635 | t2511231178,0.35,Insertions 636 | t2511231179,0.35,Insertions 637 | t2511231180,0.35,Insertions 638 | t2511231181,0.35,Insertions 639 | t2511231182,0.35,Insertions 640 | t2511231183,0.35,Insertions 641 | t2511231184,0.35,Insertions 642 | t2511231185,0.35,Insertions 643 | t2511231186,0.35,Insertions 644 | t2511231187,0.35,Insertions 645 | t2511231188,0.35,Insertions 646 | t2511231189,0.35,Insertions 647 | t2511231190,0.35,Insertions 648 | t2511231191,0.35,Insertions 649 | t2511231192,0.35,Insertions 650 | t2511231193,0.35,Insertions 651 | t2511231194,0.35,Insertions 652 | t2511231195,0.35,Insertions 653 | t2511231196,0.35,Insertions 654 | t2511231197,0.35,Insertions 655 | t2511231198,0.35,Insertions 656 | t2511231199,0.35,Insertions 657 | t2511231200,0.35,Insertions 658 | t2511231201,0.35,Insertions 659 | t2511231202,0.35,Insertions 660 | t2511231203,0.35,Insertions 661 | t2511231204,0.35,Insertions 662 | t2511231205,0.35,Insertions 663 | t2511231206,0.35,Insertions 664 | t2511231207,0.35,Insertions 665 | t2511231208,0.35,Insertions 666 | t2511231209,0.35,Insertions 667 | t2511231211,0.35,Insertions 668 | t2511231212,0.35,Insertions 669 | t2511231213,0.35,Insertions 670 | t2511231214,0.35,Insertions 671 | t2511231215,0.35,Insertions 672 | t2511231216,0.35,Insertions 673 | t2511231217,0.35,Insertions 674 | t2511231218,0.35,Insertions 675 | t2511231219,0.35,Insertions 676 | t2511231220,0.35,Insertions 677 | t2512047078,0.35,Insertions 678 | t2511231222,0.35,Insertions 679 | t2512047016,0.35,Insertions 680 | t2512047018,0.35,Insertions 681 | t2512047033,0.35,Insertions 682 | t2512047034,0.35,Insertions 683 | t2512047035,0.35,Insertions 684 | t2512047036,0.35,Insertions 685 | t2512047037,0.35,Insertions 686 | t2512047038,0.35,Insertions 687 | t2512047040,0.35,Insertions 688 | t2512047041,0.35,Insertions 689 | t2512047042,0.35,Insertions 690 | t2512047043,0.35,Insertions 691 | t2512047052,0.35,Insertions 692 | t2512047053,0.35,Insertions 693 | t2512047054,0.35,Insertions 694 | t2512047055,0.35,Insertions 695 | t2512047056,0.35,Insertions 696 | t2512047057,0.35,Insertions 697 | t2512047058,0.35,Insertions 698 | t2512047059,0.35,Insertions 699 | t2512047060,0.35,Insertions 700 | t2512047061,0.35,Insertions 701 | t2512047062,0.35,Insertions 702 | t2512047063,0.35,Insertions 703 | t2512047064,0.35,Insertions 704 | t2512047065,0.35,Insertions 705 | t2512047066,0.35,Insertions 706 | t2512047067,0.35,Insertions 707 | t2512047068,0.35,Insertions 708 | t2512047069,0.35,Insertions 709 | t2512047070,0.35,Insertions 710 | t2512564045,0.35,Insertions 711 | t2512047072,0.35,Insertions 712 | t2512047073,0.35,Insertions 713 | t2512047074,0.35,Insertions 714 | t2512047075,0.35,Insertions 715 | t2512047076,0.35,Insertions 716 | t2512047077,0.35,Insertions 717 | t2512564052,0.35,Insertions 718 | t2512047079,0.35,Insertions 719 | t2512047080,0.35,Insertions 720 | t2512564056,0.35,Insertions 721 | t2512047086,0.35,Insertions 722 | t2512047087,0.35,Insertions 723 | t2512047088,0.35,Insertions 724 | t2512047089,0.35,Insertions 725 | t2512047090,0.35,Insertions 726 | t2512564009,0.35,Insertions 727 | t2512564010,0.35,Insertions 728 | t2512564011,0.35,Insertions 729 | t2512564015,0.35,Insertions 730 | t2512564016,0.35,Insertions 731 | t2512564026,0.35,Insertions 732 | t2512564027,0.35,Insertions 733 | t2512564028,0.35,Insertions 734 | t2512564029,0.35,Insertions 735 | t2512564030,0.35,Insertions 736 | t2512564031,0.35,Insertions 737 | t2512564032,0.35,Insertions 738 | t2512564033,0.35,Insertions 739 | t2512564034,0.35,Insertions 740 | t2512564035,0.35,Insertions 741 | t2512564036,0.35,Insertions 742 | t2512564037,0.35,Insertions 743 | t2512564038,0.35,Insertions 744 | t2512564039,0.35,Insertions 745 | t2512564040,0.35,Insertions 746 | t2512564041,0.35,Insertions 747 | t2512564042,0.35,Insertions 748 | t2512564043,0.35,Insertions 749 | t2512564044,0.35,Insertions 750 | t2512875024,0.35,Insertions 751 | t2512564046,0.35,Insertions 752 | t2512564047,0.35,Insertions 753 | t2512564048,0.35,Insertions 754 | t2512564049,0.35,Insertions 755 | t2512564050,0.35,Insertions 756 | t2512564051,0.35,Insertions 757 | t2512564066,0.35,Insertions 758 | t2512564053,0.35,Insertions 759 | t2512564054,0.35,Insertions 760 | t2512564069,0.35,Insertions 761 | t2512564057,0.35,Insertions 762 | t2512564058,0.35,Insertions 763 | t2512564059,0.35,Insertions 764 | t2512564060,0.35,Insertions 765 | t2512564061,0.35,Insertions 766 | t2512564062,0.35,Insertions 767 | t2512564063,0.35,Insertions 768 | t2512564064,0.35,Insertions 769 | t2512564065,0.35,Insertions 770 | t2512564079,0.35,Insertions 771 | t2512564067,0.35,Insertions 772 | t2512564068,0.35,Insertions 773 | t2512875013,0.35,Insertions 774 | t2512564070,0.35,Insertions 775 | t2512564071,0.35,Insertions 776 | t2512564072,0.35,Insertions 777 | t2512564073,0.35,Insertions 778 | t2512564074,0.35,Insertions 779 | t2512564075,0.35,Insertions 780 | t2512564076,0.35,Insertions 781 | t2512564077,0.35,Insertions 782 | t2512564078,0.35,Insertions 783 | t2512875014,0.35,Insertions 784 | t2512564080,0.35,Insertions 785 | t2512564091,0.35,Insertions 786 | t2512875026,0.35,Insertions 787 | t2512875015,0.35,Insertions 788 | t2512875016,0.35,Insertions 789 | t2512875033,0.35,Insertions 790 | t2512875034,0.35,Insertions 791 | t638154504,0.5,Refinements 792 | t646311970,0.5,Refinements 793 | t637000051,0.5,Refinements 794 | t650377989,0.5,Refinements 795 | t649989916,0.5,Refinements 796 | t651324092,0.5,Refinements 797 | t646206253,0.5,Refinements 798 | t647533241,0.5,Refinements 799 | t647533171,0.5,Refinements 800 | t647533201,0.5,Refinements 801 | t638341245,0.5,Refinements 802 | t648276752,0.5,Refinements 803 | t648276619,0.5,Refinements 804 | t647533242,0.5,Refinements 805 | t649989951,0.5,Refinements 806 | t649989914,0.5,Refinements 807 | t647533108,0.5,Refinements 808 | t642555114,0.5,Refinements 809 | t645058836,0.5,Refinements 810 | t640963044,0.5,Refinements 811 | t645951812,0.5,Refinements 812 | t646206274,0.5,Refinements 813 | t647533170,0.5,Refinements 814 | t647000328,0.5,Refinements 815 | t647533174,0.5,Refinements 816 | t647533169,0.5,Refinements 817 | t646564516,0.5,Refinements 818 | t646206263,0.5,Refinements 819 | t649989913,0.5,Refinements 820 | t645058833,0.5,Refinements 821 | t647533114,0.5,Refinements 822 | t647533230,0.5,Refinements 823 | t647000205,0.5,Refinements 824 | t646206273,0.5,Refinements 825 | t638341169,0.5,Refinements 826 | t651324033,0.5,Refinements 827 | t649633070,0.5,Refinements 828 | t651324045,0.5,Refinements 829 | t643886007,0.5,Refinements 830 | t646206259,0.5,Refinements 831 | t646564521,0.5,Refinements 832 | t649989994,0.5,Refinements 833 | t646206266,0.5,Refinements 834 | t646206272,0.5,Refinements 835 | t645951811,0.5,Refinements 836 | t650716032,0.5,Refinements 837 | t651324070,0.5,Refinements 838 | t645058700,0.5,Refinements 839 | t649633047,0.5,Refinements 840 | t643692055,0.5,Refinements 841 | t650377988,0.5,Refinements 842 | t651324091,0.5,Refinements 843 | t648028004,0.5,Refinements 844 | t649989910,0.5,Refinements 845 | t647533110,0.5,Refinements 846 | t648861003,0.5,Refinements 847 | t642791603,0.5,Refinements 848 | t647000203,0.5,Refinements 849 | t651324003,0.5,Refinements 850 | t651324014,0.5,Refinements 851 | t646206258,0.5,Refinements 852 | t651324032,0.5,Refinements 853 | t646206252,0.5,Refinements 854 | t650377983,0.5,Refinements 855 | t646206264,0.5,Refinements 856 | t648861006,0.5,Refinements 857 | t647533111,0.5,Refinements 858 | t647533113,0.5,Refinements 859 | t647000204,0.5,Refinements 860 | t643692015,0.5,Refinements 861 | t651324086,0.5,Refinements 862 | -------------------------------------------------------------------------------- /data/VertebrateGutMicrobiomes/data_clade_class.csv: -------------------------------------------------------------------------------- 1 | id,class 2 | node1659,Aves 3 | node2688,Mammalia 4 | node1688,Chelonia 5 | node1655,Crocodylomorpha 6 | node56,Amphibia 7 | node139,Lepidosauria 8 | -------------------------------------------------------------------------------- /data/VertebrateGutMicrobiomes/data_phylopic_uid.csv: -------------------------------------------------------------------------------- 1 | taxa,uid,class 2 | Phyllobates_terribilis,4679516b-405b-444f-974d-9775876716e2,Amphibia 3 | Malacochersus_tornieri,b2dfadad-fd4f-44f5-ae8d-8028059c6f14,Chelonia 4 | Varanus_indicus,ce6a78bc-3ef1-4d60-ab40-113eb84c7802,Lepidosauria 5 | Eudyptula_minor,00cccd9b-0cd7-4677-9918-eddeac5cf1c6,Aves 6 | Corvus_albus,36f21978-8394-47b3-9602-b7a41113103b,Aves 7 | Sturnella_neglecta,f783a5c3-8f88-442d-9005-42791b943d7a,Aves 8 | Dromaius_novaehollandiae,35947c43-1e5c-4003-bbaa-d352530b5af7,Aves 9 | Branta_canadensis,b677ec7b-a2ef-46be-9d78-a997a88e1a9c,Aves 10 | Columba_livia,966eed5e-b869-41b4-8de7-32286ae3656a,Aves 11 | Cacatua_moluccensis,2236b809-b54a-45a2-932f-47b2ca4b8b7e,Aves 12 | Urocolius_macrourus,926aff32-d43e-4b7e-b1f2-be1d69a7c040,Aves 13 | Passer_domesticus,3b74c3e5-1ffa-4089-95b1-371f1b71fce0,Aves 14 | Limosa_lapponica,a6a38d55-71be-43f2-b781-9a845662de20,Aves 15 | Troglodytes_troglodytes,e38c264a-8989-4e69-a6c1-7778b919980d,Aves 16 | Merganetta_armata,23c63b97-e0ab-4b43-89a4-e2358f4f09ec,Aves 17 | Melospiza_melodia,fe8d7b12-73d4-44f1-9efe-eba09eb43b08,Aves 18 | Ursus_americanus,5a5dafa2-6388-43b8-a15a-4fd21cd17594,Mammalia 19 | Panthera_tigris,5e900306-3a5e-4193-8a94-74cc765f0aaf,Mammalia 20 | Alcelaphus_buselaphus,21020aad-069b-404e-a998-77460995320f,Mammalia 21 | Rhinolophus_clivosus,18bfd2fc-f184-4c3a-b511-796aafcc70f6,Mammalia 22 | Megaptera_novaeangliae,07277c99-4477-4131-ba85-7ff9b6b77a23,Mammalia 23 | Equus_hemionus,eed9512e-fb13-46b2-a846-8b149cea7288,Mammalia 24 | Ateles_geoffroyi,aceb287d-84cf-46f1-868c-4797c4ac54a8,Mammalia 25 | Gorilla_gorilla,d9af529d-e426-4c7a-922a-562d57a7872e,Mammalia 26 | Tolypeutes_matacus,5d59b5ce-c1dd-40f6-b295-8d2629b9775e,Mammalia 27 | Macropus_rufus,a55461ac-40a5-44ba-a1ce-372df579ca28,Mammalia 28 | Varecia_variegata,d6cfb28f-136e-4a20-a5ac-8eb353c7fc4a,Mammalia 29 | Macroscelides_proboscideus,b2a34ebf-1eab-4ddc-a926-af305a20828b,Mammalia 30 | -------------------------------------------------------------------------------- /data/VertebrateGutMicrobiomes/ggtree_run.R: -------------------------------------------------------------------------------- 1 | library(ggtree) 2 | library(treeio) 3 | library(ggplot2) 4 | library(ggtreeExtra) 5 | library(tidytree) 6 | library(ggnewscale) 7 | library(ggimage) 8 | 9 | tr <- read.tree("./annotated_host_tree.tre") 10 | corda <- read.csv("./mantel.jaccard.pearson.csv") 11 | corda$r <- abs(corda$r) 12 | barda <- read.csv("./data_diet_bar.csv", check.names=F) 13 | barda <- reshape2::melt(barda, id.vars="ID", variable.name="Diet", value.name="mete") 14 | barda$Diet <- factor(barda$Diet, levels=c("Fruit","Invertebrates", 15 | "Nectar","Plants","Scavenging", 16 | "Seeds","Meat (Ectotherms)", 17 | "Meat (Endotherms)", 18 | "Meat (Fish)","Meat (Unknown)")) 19 | 20 | cladeda <- read.csv("./data_clade_class.csv", check.names=F) 21 | cladeda$id <- nodeid(tr, cladeda$id) 22 | cladeda$class <- factor(cladeda$class, levels=c("Amphibia","Chelonia","Lepidosauria", 23 | "Crocodylomorpha","Aves","Mammalia")) 24 | 25 | flightda <- read.csv("./data_flight_bar.csv") 26 | 27 | phylopicda <- read.csv("./data_phylopic_uid.csv") 28 | phylopicda$class <- factor(phylopicda$class, levels=c("Amphibia","Chelonia","Lepidosauria", 29 | "Aves","Mammalia")) 30 | 31 | p <- ggtree(tr, layout="fan", open.angle=15) 32 | 33 | p <- p %<+% corda 34 | p$data$width <- ifelse(is.na(p$data$r), 0.1, 0.6) 35 | r <- NULL 36 | p <- p + aes(color=r, size=I(width)) + 37 | scale_colour_viridis_c(name="Mantel Correlation", 38 | option="C", 39 | guide=guide_colorbar(barheight=0.6, 40 | order=4, 41 | title.position="top", 42 | label.position="bottom", 43 | direction="horizontal")) 44 | 45 | p1 <- p + 46 | geom_fruit( 47 | data=barda, 48 | geom=geom_bar, 49 | mapping=aes(x=mete, y=ID, fill=Diet), 50 | orientation="y", 51 | stat="identity", 52 | colour=NA, 53 | pwidth=0.25, 54 | offset=0.008 55 | ) + 56 | scale_fill_manual( 57 | values=c("#a6cee3","#cab2d6", 58 | "#1f78b4","#33a02c", 59 | "#6a3d9a","#b2df8a", 60 | "#fb9a99","#e31a1c", 61 | "#ff7f00","#fdbf6f"), 62 | guide=guide_legend(keywidth=0.5, keyheight=0.5, order=1) 63 | ) 64 | 65 | p2 <- p1 + 66 | new_scale_colour() + 67 | geom_cladelab( 68 | data=cladeda, 69 | mapping=aes(node=id, label=class, colour=class), 70 | textcolour=NA, 71 | barsize=4, 72 | extend=0.2, 73 | offset=100) + 74 | scale_colour_manual( 75 | name="Host Class", 76 | values=c("#b2df8a","#33a02c","#fb9a99", 77 | "#e31a1c","#EACB47","#6a3d9a"), 78 | guide=guide_legend(keywidth=0.5, keyheight=0.5, order=2, 79 | override.aes=list(size=3,alpha=1)) 80 | ) 81 | 82 | p3 <- p2 + 83 | new_scale_fill() + 84 | geom_fruit( 85 | data=flightda, 86 | geom=geom_tile, 87 | mapping=aes(y=ID, fill=flight), 88 | size=0, 89 | width=14, 90 | offset=0.11, 91 | pwidth=0.4, 92 | ) + 93 | scale_fill_manual( 94 | name="Flight Status", 95 | values=c("black", "white"), 96 | guide=guide_legend(keywidth=0.5, keyheight=0.5, order=3, 97 | override.aes=list(color="black", size=0.3))) 98 | p4 <- p3 + 99 | new_scale_colour() + 100 | geom_fruit( 101 | data=phylopicda, 102 | geom=geom_phylopic, 103 | mapping=aes(y=taxa, image=uid, color=class), 104 | size=0.035, 105 | offset=0.16, 106 | alpha=0.8, 107 | position=position_identityx() 108 | ) + 109 | scale_colour_manual( 110 | values=c("#b2df8a","#33a02c","#fb9a99", 111 | "#EACB47","#6a3d9a"), 112 | guide="none" 113 | )+ 114 | theme( 115 | legend.background=element_rect(fill=NA), 116 | legend.title=element_text(size=9), 117 | legend.text=element_text(size=6.6), 118 | legend.spacing.y = unit(0.02, "cm") 119 | ) 120 | 121 | svg("tree_plot.svg") 122 | p4 123 | dev.off() 124 | -------------------------------------------------------------------------------- /data/VertebrateGutMicrobiomes/mantel.jaccard.pearson.csv: -------------------------------------------------------------------------------- 1 | ,r,p 2 | node42,0.014781426712449457,0.948 3 | node47,-0.038694550470678137,0.794 4 | 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2 | -------------------------------------------------------------------------------- /rawdata/Arabidopsis_leaf_microbiome/EMS87355-supplement-Supplementary_Tables.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/plotting-tree-with-data-using-ggtreeExtra/4e089aa5caea12c3e6110e07dbb257c7b6e25214/rawdata/Arabidopsis_leaf_microbiome/EMS87355-supplement-Supplementary_Tables.xlsx -------------------------------------------------------------------------------- /rawdata/Methanotroph/Methanotroph_rpS3_Metadata.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/plotting-tree-with-data-using-ggtreeExtra/4e089aa5caea12c3e6110e07dbb257c7b6e25214/rawdata/Methanotroph/Methanotroph_rpS3_Metadata.csv -------------------------------------------------------------------------------- /scripts/create_tree_and_dataframe.R: -------------------------------------------------------------------------------- 1 | ## This script was designed to extract the tree and associated data of tip labels of tree. 2 | ## And it should be run in the dir with > R(4.0) 3 | library(tidyverse) 4 | library(openxlsx) 5 | 6 | convert1 = "python -c 'from Bio import Phylo;Phylo.convert(\"../rawdata/HMP_tree/hmptree.xml\", \"phyloxml\", \"../data/HMP_tree/hmptree.nwk\", \"newick\")'" 7 | convert2 = "python -c 'from Bio import Phylo;Phylo.convert(\"../rawdata/PhyloPhlAn/ppa_tol.xml\", \"phyloxml\", \"../data/PhyloPhlAn/ppal_tol.nwk\", \"newick\")'" 8 | convert3 = "python -c 'from Bio import Phylo;Phylo.convert(\"../rawdata/kegg/kegg.xml\", \"phyloxml\", \"../data/kegg/kegg.nwk\", \"newick\")'" 9 | system(convert1) 10 | system(convert2) 11 | system(convert3) 12 | 13 | ################################################### 14 | ##### HMP_tree tip datasets and ring datasets ##### 15 | df <- read.table("../rawdata/HMP_tree/annot.txt", sep="\t", comment.char="", fill=TRUE, 16 | col.names=paste0("V", seq_len(4)), header=FALSE) 17 | 18 | data <- df %>% filter(V2=="ring_height" & V3==8) 19 | dat <- df %>% filter(V2=="ring_color" & V3==8) 20 | dt <- df %>% filter(V1=="ring_label_color") 21 | dd <- df %>% filter(V1=="ring_label" & V3!="Abundance when present") 22 | ddt <- merge(dt, dd, by.x="V2", by.y="V2") 23 | datt <- merge(dat, ddt, by.x="V4", by.y="V3.x") %>% select(c("V1", "V3.y")) 24 | dat1 <- merge(datt, data, by.x="V1", by.y="V1") 25 | dat1 <- merge(datt, data, by.x="V1", by.y="V1") 26 | dat1 <- dat1 %>% select(c("V1", "V3.y", "V4")) %>% rename(ID="V1", Sites="V3.y", HigherAbundance="V4") 27 | 28 | data <- df %>% filter(V2=="ring_alpha" & V3!=8) %>% select(c("V1", "V3", "V4")) 29 | dat2 <- merge(data, dd, by.x="V3", by.y="V2") %>% select(c("V1.x", "V3.y", "V4.x")) %>% 30 | rename(ID="V1.x", Abundance="V4.x", Sites="V3.y") 31 | dat2$Abundance <- as.numeric(dat2$Abundance) 32 | 33 | dd1 <- df %>% filter(V2=="clade_marker_color") 34 | dd2 <- dd1[grep("t6", dd1$V1),] 35 | dd3 <- dd1[!grepl("t6", dd1$V1),] 36 | dd1 <- merge(dd2, dd3, by.x="V3", by.y="V3") %>% select(c("V1.x", "V1.y")) %>% rename(ID="V1.x", Phylum="V1.y") 37 | ddtt <- df %>% filter(V2=="clade_marker_shape") %>% select(c("V1")) %>% rename(ID="V1") %>% 38 | mutate(Type="Potential pathogens") 39 | ddtt1 <- data.frame(ID=as.vector(dd1[!dd1$ID %in% ddtt$ID,"ID"])) %>% mutate(Type="Commensal microbes") 40 | ddtt2 <- df %>% filter(V2=="clade_marker_size") %>% select(c("V1", "V3")) %>% rename(ID="V1", Size="V3") 41 | ddtt2 <- ddtt2[grep("t6", ddtt2$ID),] 42 | ddtt <- rbind(ddtt1, ddtt) 43 | dat3 <- merge(dd1, ddtt, by.x="ID", by.y="ID") 44 | dat3 <- merge(dat3, ddtt2, by.x="ID", by.y="ID") 45 | dat3$Size <- as.numeric(dat3$Size) 46 | dat1$Sites <- factor(dat1$Sites, levels=c("Stool (prevalence)", "Cheek (prevalence)", 47 | "Plaque (prevalence)", "Tongue (prevalence)", 48 | "Nose (prevalence)", "Vagina (prevalence)", 49 | "Skin (prevalence)")) 50 | dat2$Sites <- factor(dat2$Sites, levels=c("Stool (prevalence)", "Cheek (prevalence)", 51 | "Plaque (prevalence)", "Tongue (prevalence)", 52 | "Nose (prevalence)", "Vagina (prevalence)", 53 | "Skin (prevalence)")) 54 | 55 | write.table(dat3, "../data/HMP_tree/tippoint_attr.csv", sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE) 56 | write.table(dat2, "../data/HMP_tree/ringheatmap_attr.csv", sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE) 57 | write.table(dat1, "../data/HMP_tree/barplot_attr.csv", sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE) 58 | ################################################### 59 | ################################################### 60 | 61 | ################################################### 62 | #### PhyloPhlAn tip datasets and ring datasets #### 63 | df <- read.table("../rawdata/PhyloPhlAn/annot.txt", sep="\t", comment.char="", fill=TRUE, 64 | col.names=paste0("V", seq_len(4)), header=FALSE) 65 | data <- df %>% filter(V2=="clade_marker_color") 66 | data1 <- data[grepl("^t", data$V1),] %>% select(c("V1", "V3")) 67 | #head(data1) 68 | data2 <- data[!grepl("^t", data$V1),] %>% 69 | filter(V3 !="k") %>% select(c("V1", "V3")) 70 | #data2 <- rbind(data2, data.frame(V1="Others", V3="Black")) 71 | dt <- merge(data1, data2, by.x="V3", by.y="V3") %>%select("V1.x", "V1.y") %>% 72 | rename(ID="V1.x", Phylum="V1.y") 73 | dt2 <- dt %>% rename(Phyla="Phylum") 74 | 75 | # data for the tip points. 76 | dat <- df %>% filter(V2=="ring_height" & V3==1) %>% select(c("V1", "V4")) %>% 77 | rename(ID="V1", Abundance="V4") 78 | dat <- merge(dat, dt2, by.x="ID", by.y="ID",all.x=TRUE) 79 | dat[is.na(dat$Phyla),"Phyla"] <- "Other" 80 | dat$Abundance <- as.numeric(dat$Abundance) 81 | # data for the bar plot of first ring. 82 | # data for the point plot of second ring. 83 | dag <- data.frame(color=c("b", "k", "r", "g"), 84 | Type=c("Mislabelled", "Insertions", "Refinements", "Corrections")) 85 | da1 <- df %>% filter(V2=="ring_color" & V3==2) %>% select(c("V1", "V4")) %>% 86 | rename(ID="V1", color="V4") %>% distinct() 87 | da2 <- df %>% filter(V2=="ring_height" & V3==2) %>% select(c("V1", "V4")) %>% 88 | rename(ID="V1", Pos="V4") %>% distinct() 89 | da <- merge(da1, da2, by="ID") 90 | da <- merge(da, dag, by="color") %>% select(c("ID","Pos","Type")) %>% 91 | distinct() 92 | 93 | da$Pos <- as.numeric(da$Pos) 94 | da$Type <- factor(da$Type, levels=c("Mislabelled", "Insertions", "Corrections", "Refinements")) 95 | 96 | write.table(dt, "../data/PhyloPhlAn/tippoint_attr.csv", sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE) 97 | write.table(dat, "../data/PhyloPhlAn/barplot_attr.csv", sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE) 98 | write.table(da, "../data/PhyloPhlAn/ringpoint_attr.csv", sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE) 99 | ################################################### 100 | ################################################### 101 | 102 | ################################################### 103 | #### kegg tip datasets and ring datasets #### 104 | df <- read.table("../rawdata/kegg/annot.txt", sep="\t", check.names=FALSE, comment.char="", fill=TRUE, 105 | col.names=paste0("V", seq_len(4)), stringsAsFactors=FALSE) 106 | #head(dat) 107 | data <- df %>% filter(V2=="clade_marker_color") 108 | data1 <- data[nchar(as.vector(data$V1))<4,] %>% select(c("V1", "V3")) 109 | data1[as.vector(data1$V3)=="k", "V3"] <- "Black" 110 | data2 <- data[nchar(as.vector(data$V1))>4,] %>% select(c("V1", "V3")) 111 | data2 <- data2[order(as.vector(data2$V1)),,drop=FALSE] 112 | tmp <- data2$V1 113 | data2 <- rbind(data2, data.frame(V1="Other", V3="Black")) 114 | data2$V1 <- factor(data2$V1, levels=c(tmp,"Other")) 115 | 116 | dt <- merge(data1, data2, by.x="V3", by.y="V3") %>% select("V1.x", "V1.y") %>% 117 | rename(ID="V1.x", Phyla="V1.y") 118 | 119 | 120 | dat1 <- df %>% filter(V2=="ring_color" & V3 %in% as.character(seq_len(8))) %>% 121 | select(c("V1", "V3")) %>% rename(ID="V1", ring="V3") %>% mutate(Type1="V/A-type ATPase") 122 | dat2 <- df %>% filter(V2=="ring_color" & V3 %in% as.character(c(9:16))) %>% 123 | select(c("V1", "V3")) %>% rename(ID="V1", ring="V3") %>% mutate(Type1="F-type ATPase") 124 | dat <- rbind(dat1, dat2) 125 | #dat$Type1 <- factor(dat$Type1, levels=c("V/A-type ATPase", "F-type ATPase")) 126 | dat$ring <- as.numeric(dat$ring) 127 | 128 | dda1 <- df %>% filter(V2=="ring_color" & V3 %in% as.character(17:21)) %>% 129 | select(c("V1", "V4")) %>% rename(ID="V1", color="V4") 130 | dda2 <- df %>% filter(V2=="ring_alpha") %>% select(c("V1", "V4")) %>% 131 | rename(ID="V1", Abundance="V4") 132 | dda3 <- data.frame(Type2=c("FA synth init", "FA synth elong", "acyl-CoA synth", "beta-Oxidation", "Ketone biosynth"), 133 | color=c("#b22222", "#005500", "#0000be", "#9f1f9f", "#793a07")) 134 | dda3$Type2 <- factor(dda3$Type2, levels=c("FA synth init", "FA synth elong", "acyl-CoA synth", "beta-Oxidation", "Ketone biosynth")) 135 | 136 | dda <- merge(dda1, dda2, by.x="ID", by.y="ID") 137 | dda <- merge(dda, dda3, by="color") 138 | dda$Abundance <- as.numeric(dda$Abundance) 139 | dda$color <- NULL 140 | 141 | dd1 <- df %>% filter(V2=="ring_height" & V3 == "22") %>% select(c("V1", "V4")) %>% 142 | rename(ID="V1", Length="V4") 143 | dd <- merge(dd1, data1, by.x="ID", by.y="V1") 144 | dd <- merge(dd, data2, by.x="V3", by.y="V3") %>% 145 | select(c("ID", "Length"#, "V1" 146 | )) #%>% 147 | #rename(Phyla="V1") 148 | dd$Length <- as.numeric(dd$Length) 149 | 150 | write.table(dt, "../data/kegg/tippoint_attr.csv", sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE) 151 | write.table(dat, "../data/kegg/firstring_attr.csv", sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE) 152 | write.table(dda, "../data/kegg/secondring_attr.csv", sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE) 153 | write.table(dd, "../data/kegg/barplot_attr.csv", sep=",", row.names=FALSE, col.names=TRUE, quote=FALSE) 154 | ################################################### 155 | ## The methanotroph metadata 156 | ################################################### 157 | metada <- read.csv("../rawdata/Methanotroph/Methanotroph_rpS3_Metadata.csv") 158 | metada <- metada[is.na(metada$Outgroup),] 159 | 160 | metada$Specific.Ecosystem[metada$Specific.Ecosystem %in% c("Contaminated", "Wastewater")] <- "Contaminated/Wastewater" 161 | metada$Specific.Ecosystem[metada$Specific.Ecosystem == c("Bathymodiolus Endosymbiont")] <- "Endosymbiont" 162 | metada$Specific.Ecosystem[metada$Specific.Ecosystem %in% c("Ground Water", "Drinking Water", "River Sediment", "Lake Water", "Lake Sediment")] <- "Freshwater" 163 | metada$Specific.Ecosystem[metada$Specific.Ecosystem %in% c("Marine Water", "Marine Sediment")] <- "Marine" 164 | metada$MetaType[metada$MetaType%in%c("MetaG", "MAG")] <- "Metagenome" 165 | metada$MetaType[metada$MetaType=="SAG"] <- "Single-amplified genome" 166 | metada$MetaType[metada$MetaType=="MetaT"] <- "Metatranscriptome" 167 | 168 | metada <- metada[,colnames(metada) %in% c("Name.in.Fastas", "Specific.Ecosystem", "MetaType", "Treatment")] 169 | write.table(metada, file="../data/Methanotroph/metadata.csv", row.names=FALSE, quote=FALSE, sep=",") 170 | 171 | ################################################## 172 | ################################################## 173 | 174 | ################################################## 175 | ##### Arabidopsis leaf microbiome datasets #### 176 | da <- read.xlsx("../rawdata/Arabidopsis_leaf_microbiome/EMS87355-supplement-Supplementary_Tables.xlsx", startRow=2) 177 | dat <- read.xlsx("../rawdata/Arabidopsis_leaf_microbiome/EMS87355-supplement-Supplementary_Tables.xlsx", sheet=2, startRow=4) 178 | df <- read.xlsx("../rawdata/Arabidopsis_leaf_microbiome/EMS87355-supplement-Supplementary_Tables.xlsx", sheet=9, startRow=3) 179 | 180 | df <- df[-c(208:210),c(1, 3:11)] 181 | df1 <- df[,c(1:9)] 182 | df2 <- df[,c(1,10)] 183 | df1 <- df1 %>% gather(key="BGCs", value="Count", -Strain) 184 | df1$Strain <- paste0("s__", df1$Strain) 185 | 186 | colnames(dat) <- c("Strain", "Genus", "Strong.I", "Weak.I", "Total.I", 187 | "Strong.S", "Weak.S", "Total.S", "Total_interactions") 188 | 189 | dat <- dat %>% distinct() %>% 190 | select(c("Strain", "Strong.I", "Weak.I", "Strong.S", "Weak.S")) 191 | dat <- dat %>% gather(key="key", value="value", -Strain) %>% 192 | separate(key, c("Weight", "Type")) %>% 193 | mutate(Type=gsub("I", "Inhibitor", Type)) %>% 194 | mutate(Type=gsub("S", "Sensitive", Type)) %>% 195 | unite("Number", Type:Weight, remove=TRUE, sep=" ") 196 | dat$Strain <- paste0("s__", dat$Strain) 197 | 198 | da1 <- da[,grepl("Inhibitor", colnames(da))] %>% 199 | distinct() %>% 200 | rename(Leaf = Inhibitor) 201 | 202 | colnames(da1) <- gsub("\\.Inhibitor", "", colnames(da1)) 203 | 204 | da2 <- da[,grepl("Sensitive", colnames(da))] %>% 205 | distinct() %>% 206 | rename(Leaf=Sensitive) 207 | colnames(da2) <- gsub("\\.Sensitive", "", colnames(da2)) 208 | 209 | da1_2 <- rbind(da1, da2) %>% distinct() 210 | da1_2$Isolation <- da1_2$Leaf 211 | da1_2$Leaf <- NULL 212 | da1_2$Kindom <- "Bacteria" 213 | da1_2 <- da1_2[,c(7, seq_len(6))] 214 | 215 | da1_tmp <- data.frame(Kindom="Bacteria",Phylum="Firmicutes",Class="Bacilli", 216 | Order="Bacillales",Family="Bacillaceae",Genus="Bacillus",Isolation="Leaf406") 217 | da1_2 <- rbind(da1_2, da1_tmp) 218 | da3 <- da[,c(1, 2, 3)] 219 | da3$Inhibitor <- paste0("s__", da3$Inhibitor) 220 | da3$Sensitive <- paste0("s__", da3$Sensitive) 221 | #da3$Interaction <- unlist(lapply(da3$Interaction,function(x) unlist(strsplit(x,split=";"))[1])) 222 | 223 | daphycla1 <- da1_2 %>% 224 | filter(Phylum %in% c("Actinobacteria", "Bacteroidetes", "Firmicutes", "Deinococcus-Thermus")) %>% 225 | select(c("Isolation", "Phylum")) %>% 226 | rename(Taxa="Phylum") %>% 227 | mutate(Level="Phylum") #%>% 228 | # mutate(Taxa=gsub("Deinococcus-Thermus", "Firmicutes", Taxa)) 229 | 230 | daphycla2 <- da1_2 %>% 231 | filter(Phylum=="Proteobacteria") %>% 232 | select("Isolation", "Class") %>% 233 | rename(Taxa="Class") %>% 234 | mutate(Level="Class") 235 | 236 | daphycla <- rbind(daphycla1, daphycla2) 237 | daphycla$Isolation <- paste0("s__", daphycla$Isolation) 238 | 239 | write.csv(da1_2, "../data/Arabidopsis_leaf_microbiome/all_stain_taxonomy.csv", row.names=FALSE, quote=FALSE) 240 | write.csv(da3, "../data/Arabidopsis_leaf_microbiome/Interaction_link_tab.csv", row.names=FALSE, quote=FALSE) 241 | write.csv(dat, "../data/Arabidopsis_leaf_microbiome/Interaction_weight.csv", row.names=FALSE, quote=FALSE) 242 | write.csv(daphycla, "../data/Arabidopsis_leaf_microbiome/stain_tippoint.csv", row.names=FALSE, quote=FALSE) 243 | write.csv(df1, "../data/Arabidopsis_leaf_microbiome/BGCs_heatmap.csv", row.names=FALSE, quote=FALSE) 244 | --------------------------------------------------------------------------------