├── .gitignore ├── LICENSE ├── Manual ├── Metmapr tutorial v1.doc ├── Metmapr v1.2.1 tutorial v1.doc.pdf ├── metamapr_long.gif └── test.html ├── MetaMapR.Rproj ├── NEWS.md ├── README.Rmd ├── README.html ├── README.md ├── README_files ├── bootstrap-2.3.2 │ ├── css │ │ ├── bootstrap-responsive.css │ │ ├── bootstrap-responsive.min.css │ │ ├── bootstrap.css │ │ ├── bootstrap.min.css │ │ ├── cerulean.min.css │ │ ├── cosmo.min.css │ │ ├── flatly.min.css │ │ ├── fonts │ │ │ ├── Lato.ttf │ │ │ ├── LatoBlack.ttf │ │ │ ├── LatoBold.ttf │ │ │ ├── LatoItalic.ttf │ │ │ ├── Lora.ttf │ │ │ ├── LoraBold.ttf │ │ │ ├── LoraBoldItalic.ttf │ │ │ ├── LoraItalic.ttf │ │ │ ├── NewsCycle.ttf │ │ │ ├── NewsCycleBold.ttf │ │ │ ├── OpenSans.ttf │ │ │ ├── OpenSansBold.ttf │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ ├── OpenSansItalic.ttf │ │ │ ├── OpenSansLight.ttf │ │ │ ├── OpenSansLightItalic.ttf │ │ │ ├── RalewayBold.ttf │ │ │ ├── Telex.ttf │ │ │ └── Ubuntu.ttf │ │ ├── journal.min.css │ │ ├── readable.min.css │ │ ├── spacelab.min.css │ │ └── united.min.css │ ├── img │ │ ├── glyphicons-halflings-white.png │ │ └── glyphicons-halflings.png │ └── js │ │ ├── bootstrap.js │ │ └── bootstrap.min.js ├── highlight │ ├── default.css │ ├── highlight.js │ └── textmate.css └── jquery-1.11.0 │ └── jquery.min.js ├── SVGnetwork.html ├── screenshots.md ├── version.Rmd ├── version.html ├── version.md ├── version_files ├── bootstrap-2.3.2 │ ├── css │ │ ├── bootstrap-responsive.css │ │ ├── bootstrap-responsive.min.css │ │ ├── bootstrap.css │ │ ├── bootstrap.min.css │ │ ├── cerulean.min.css │ │ ├── cosmo.min.css │ │ ├── flatly.min.css │ │ ├── fonts │ │ │ ├── Lato.ttf │ │ │ ├── LatoBlack.ttf │ │ │ ├── LatoBold.ttf │ │ │ ├── LatoItalic.ttf │ │ │ ├── Lora.ttf │ │ │ ├── LoraBold.ttf │ │ │ ├── LoraBoldItalic.ttf │ │ │ ├── LoraItalic.ttf │ │ │ ├── NewsCycle.ttf │ │ │ ├── NewsCycleBold.ttf │ │ │ ├── OpenSans.ttf │ │ │ ├── OpenSansBold.ttf │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ ├── OpenSansItalic.ttf │ │ │ ├── OpenSansLight.ttf │ │ │ ├── OpenSansLightItalic.ttf │ │ │ ├── RalewayBold.ttf │ │ │ ├── Telex.ttf │ │ │ └── Ubuntu.ttf │ │ ├── journal.min.css │ │ ├── readable.min.css │ │ ├── spacelab.min.css │ │ └── united.min.css │ ├── img │ │ ├── glyphicons-halflings-white.png │ │ └── glyphicons-halflings.png │ └── js │ │ ├── bootstrap.js │ │ └── bootstrap.min.js ├── highlight │ ├── default.css │ ├── highlight.js │ └── textmate.css └── jquery-1.11.0 │ └── jquery.min.js ├── version_info ├── version_info.txt └── www ├── css ├── bootstrap.css └── style.css ├── d3label.html ├── favicon.ico ├── images ├── about_page_example.png ├── black_logo.jpg ├── data_page_example.png ├── export_page_example.png ├── network_page_example.png └── progressauto.gif ├── js ├── busy.js ├── navbar.js └── timer.js └── navbar.html /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | packrat/lib*/ 5 | -------------------------------------------------------------------------------- /Manual/Metmapr tutorial v1.doc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dgrapov/MetaMapR/c98465fb02479b9faca3775036fce1a15a869079/Manual/Metmapr tutorial v1.doc -------------------------------------------------------------------------------- /Manual/Metmapr v1.2.1 tutorial v1.doc.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dgrapov/MetaMapR/c98465fb02479b9faca3775036fce1a15a869079/Manual/Metmapr v1.2.1 tutorial v1.doc.pdf -------------------------------------------------------------------------------- /Manual/metamapr_long.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dgrapov/MetaMapR/c98465fb02479b9faca3775036fce1a15a869079/Manual/metamapr_long.gif -------------------------------------------------------------------------------- /MetaMapR.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | 15 | BuildType: Package 16 | PackageUseDevtools: Yes 17 | PackageInstallArgs: --no-multiarch --with-keep.source 18 | -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- 1 | ### Features and Fixes 2 | #### version 1.4 (1/18/15) 3 | * updated logo and CSS styling 4 | * updated About 5 | * added screenshots 6 | #### version 1.3.1 (11/19/14) 7 | * fixed CTS translations 8 | * added ID merging for additive translations 9 | * added column removal to dataset managment 10 | * added package installation of WGCNA and Chemminer, previously missing dependancies 11 | 12 | #### version 1.3 (09/23/14) 13 | * added interactive network visualization using D3.js 14 | * added network output as svg 15 | * added metabolite SDF file caching for faster structural similarity calculations 16 | * decoupled edge list calculation and filtering on weight 17 | * switched to fluidRow layout in shiny UI 18 | * removed double translation bug 19 | * added new progress indicator 20 | -------------------------------------------------------------------------------- /README.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "README" 3 | output: 4 | html_document: 5 | keep_md: yes 6 | self_contained: no 7 | --- 8 | 9 | ```{r, echo=FALSE} 10 | info<-data.frame(read.table("version_info.txt",header=TRUE)) 11 | ``` 12 | 13 | [MetaMapR](http://dgrapov.github.io/MetaMapR/) 14 | ======== 15 | 16 | ## A metabolomic network mapping tool 17 |  18 | 19 | ## [Screenshots](https://github.com/dgrapov/MetaMapR/blob/master/screenshots.md) 20 | 21 | ### Installation 22 | Requires [R](http://cran.us.r-project.org/) and [Shiny](https://github.com/rstudio/shiny-server). 23 | Try it out using the [Shiny glimmer server](http://spark.rstudio.com/dgrapov/MetaMapR/) 24 | or run locally by pasting the following code into the R console: 25 | ```r 26 | library(shiny) 27 | shiny::runGitHub('MetaMapR','dgrapov') 28 | ``` 29 | Alternatively download the .zip file, unzip and run the following code (example for file on desktop) 30 | ```r 31 | library(shiny) 32 | shiny::runApp('~/../Desktop/MetaMapR-master/MetaMapR-master') 33 | ``` 34 | NOTE: modify file paths for OSX and LINUX 35 | 36 | ### Instructions 37 | * [Tutorial](http://ufpr.dl.sourceforge.net/project/metamapr/Metmapr%20v1.2.1%20tutorial%20v1.doc.pdf) (a more detailed version coming soon) 38 | * [Examples](http://dgrapov.github.io/MetaMapR/) 39 | 40 | ### Information 41 | Version: `r info$version` (`r info$date`) 42 | 43 | News: [See the newest features.](https://github.com/dgrapov/MetaMapR/blob/master/NEWS.md) 44 | 45 | License: GNU General Public License (v3), [read more](https://github.com/dgrapov/MetaMapR/blob/master/LICENSE) 46 | 47 | ### Citation 48 | If you find MetaMapR useful please cite this tool using the doi listed below. 49 | 50 | Dmitry Grapov (2014) MetaMapR: Metabolomic Network Analysis and Visualization Tool 51 | 52 | [](http://dx.doi.org/10.5281/zenodo.12880) 53 | 54 | ### TODO 55 | * add partial correlations 56 | * add cytoscape.js networks 57 | * enable network mapping 58 | 59 | ### FAQ 60 | 1. How are multiple edge types handled in the network output? 61 | 62 | The default setting for returning all edge types or only unique edges can be found under the network tab using the unique edges checkbox. If the option is selected then edges are returned based on a hierarchy Biochemical > Structural > Mass Spectral > Correlation, otherwise all edges are returned. -------------------------------------------------------------------------------- /README.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 |
6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 |Requires R and Shiny. Try it out using the Shiny glimmer server or run locally by pasting the following code into the R console:
71 |library(shiny)
72 | shiny::runGitHub('MetaMapR','dgrapov')
73 | Alternatively download the .zip file, unzip and run the following code (example for file on desktop)
74 |library(shiny)
75 | shiny::runApp('~/../Desktop/MetaMapR-master/MetaMapR-master')
76 | NOTE: modify file paths for OSX and LINUX
77 |Version: 1.4.0 (1/18/2015)
88 |News: See the newest features.
89 |License: GNU General Public License (v3), read more
90 |If you find MetaMapR useful please cite this tool using the doi listed below.
94 |Dmitry Grapov (2014) MetaMapR: Metabolomic Network Analysis and Visualization Tool
95 | 96 |The default setting for returning all edge types or only unique edges can be found under the network tab using the unique edges checkbox. If the option is selected then edges are returned based on a hierarchy Biochemical > Structural > Mass Spectral > Correlation, otherwise all edges are returned.
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