├── .Rbuildignore ├── .github └── workflows │ └── no-response.yml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── bigPint.R ├── convertSEPair.R ├── convertSESubsetGenes.R ├── data-se_soybean_cn_sub.R ├── data-se_soybean_ir_sub.R ├── data-soybean_cn.R ├── data-soybean_cn_metrics.R ├── data-soybean_cn_sub.R ├── data-soybean_cn_sub_metrics.R ├── data-soybean_ir.R ├── data-soybean_ir_metrics.R ├── data-soybean_ir_sub.R ├── data-soybean_ir_sub_metrics.R ├── helperCadFALSE.R ├── helperCadFALSEPair.R ├── helperCadTRUE.R ├── helperCadTRUEPair.R ├── helperGetData.R ├── helperMakeHex.R ├── helperMakeHexDF.R ├── helperMakePairs.R ├── helperSMFC.R ├── helperSMHex.R ├── helperSMOrth.R ├── helperSMPoints.R ├── helperSMPrint.R ├── helperTestData.R ├── helperTestDataMetrics.R ├── helperTestDataMetricsLitreApp.R ├── helperTestDataMetricsVolcano.R ├── helperTestDataMetricsVolcanoApp.R ├── helperTestHaveData.R ├── helperTestHaveDataMetrics.R ├── plotClusters.R ├── plotLitre.R ├── plotLitreApp.R ├── plotPCP.R ├── plotPCPApp.R ├── plotSM.R ├── plotSMApp.R ├── plotVolcano.R └── plotVolcanoApp.R ├── README.md ├── _pkgdown.yml ├── data ├── datalist ├── se_soybean_cn_sub.rda ├── se_soybean_ir_sub.rda ├── soybean_cn.rda ├── soybean_cn_metrics.rda ├── soybean_cn_sub.rda ├── soybean_cn_sub_metrics.rda ├── soybean_ir.rda ├── soybean_ir_metrics.rda ├── soybean_ir_sub.rda └── soybean_ir_sub_metrics.rda ├── docs ├── 404.html ├── CNAME ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── bioconductor.html │ ├── clusters.html │ ├── clusters_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-5-2.png │ │ │ └── unnamed-chunk-6-1.png │ ├── createDataMetrics.html │ ├── data.html │ ├── dataMetrics.html │ ├── honeybee.html │ ├── index.html │ ├── installation.html │ ├── interactive.html │ ├── manuscripts.html │ ├── methods.html │ ├── pipeline.html │ ├── pipeline_files │ │ ├── crosstalk-1.0.0 │ │ │ ├── css │ │ │ │ └── crosstalk.css │ │ │ └── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ ├── crosstalk-1.1.0.1 │ │ │ ├── css │ │ │ │ └── crosstalk.css │ │ │ └── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ ├── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-28-1.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-7-1.png │ │ ├── htmlwidgets-1.3 │ │ │ └── htmlwidgets.js │ │ ├── htmlwidgets-1.5.1 │ │ │ └── htmlwidgets.js │ │ ├── jquery-1.11.3 │ │ │ ├── jquery-AUTHORS.txt │ │ │ ├── jquery.js │ │ │ ├── jquery.min.js │ │ │ └── jquery.min.map │ │ ├── plotly-binding-4.8.0 │ │ │ └── plotly.js │ │ ├── plotly-binding-4.9.0 │ │ │ └── plotly.js │ │ ├── plotly-binding-4.9.1 │ │ │ └── plotly.js │ │ ├── plotly-binding-4.9.2.1 │ │ │ └── plotly.js │ │ ├── plotly-binding-4.9.2 │ │ │ └── plotly.js │ │ ├── plotly-htmlwidgets-css-1.39.2 │ │ │ └── plotly-htmlwidgets.css │ │ ├── plotly-htmlwidgets-css-1.46.1 │ │ │ └── plotly-htmlwidgets.css │ │ ├── plotly-htmlwidgets-css-1.49.4 │ │ │ └── plotly-htmlwidgets.css │ │ ├── plotly-htmlwidgets-css-1.52.2 │ │ │ └── plotly-htmlwidgets.css │ │ ├── plotly-main-1.39.2 │ │ │ └── plotly-latest.min.js │ │ ├── plotly-main-1.46.1 │ │ │ └── plotly-latest.min.js │ │ ├── plotly-main-1.49.4 │ │ │ └── plotly-latest.min.js │ │ ├── plotly-main-1.52.2 │ │ │ └── plotly-latest.min.js │ │ └── typedarray-0.1 │ │ │ └── typedarray.min.js │ ├── plotIntro.html │ ├── plotIntro_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── static.html │ ├── static_files │ │ ├── crosstalk-1.0.0 │ │ │ ├── css │ │ │ │ └── crosstalk.css │ │ │ └── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ ├── crosstalk-1.1.0.1 │ │ │ ├── css │ │ │ │ └── crosstalk.css │ │ │ └── js │ │ │ │ ├── crosstalk.js │ │ │ │ ├── crosstalk.js.map │ │ │ │ ├── crosstalk.min.js │ │ │ │ └── crosstalk.min.js.map │ │ ├── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-10-2.png │ │ │ ├── unnamed-chunk-10-3.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-7-1.png │ │ ├── htmlwidgets-1.3 │ │ │ └── htmlwidgets.js │ │ ├── htmlwidgets-1.5.1 │ │ │ └── htmlwidgets.js │ │ ├── jquery-1.11.3 │ │ │ ├── jquery-AUTHORS.txt │ │ │ ├── jquery.js │ │ │ ├── jquery.min.js │ │ │ └── jquery.min.map │ │ ├── plotly-binding-4.8.0 │ │ │ └── plotly.js │ │ ├── plotly-binding-4.9.0 │ │ │ └── plotly.js │ │ ├── plotly-binding-4.9.1 │ │ │ └── plotly.js │ │ ├── plotly-binding-4.9.2.1 │ │ │ └── plotly.js │ │ ├── plotly-binding-4.9.2 │ │ │ └── plotly.js │ │ ├── plotly-htmlwidgets-css-1.39.2 │ │ │ └── plotly-htmlwidgets.css │ │ ├── plotly-htmlwidgets-css-1.46.1 │ │ │ └── plotly-htmlwidgets.css │ │ ├── plotly-htmlwidgets-css-1.49.4 │ │ │ └── plotly-htmlwidgets.css │ │ ├── plotly-htmlwidgets-css-1.52.2 │ │ │ └── plotly-htmlwidgets.css │ │ ├── plotly-main-1.39.2 │ │ │ └── plotly-latest.min.js │ │ ├── plotly-main-1.46.1 │ │ │ └── plotly-latest.min.js │ │ ├── plotly-main-1.49.4 │ │ │ └── plotly-latest.min.js │ │ ├── plotly-main-1.52.2 │ │ │ └── plotly-latest.min.js │ │ └── typedarray-0.1 │ │ │ └── typedarray.min.js │ ├── summarizedExperiment.html │ ├── superimposeData.html │ └── superimposeData_files │ │ └── figure-html │ │ ├── unnamed-chunk-1-1.png │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-3-1.png │ │ └── unnamed-chunk-4-1.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── docsearch.json ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── index.html ├── link.svg ├── logo.png ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── N_P_Glyma.05G188700.Wm82.a2.v1_litre.jpg │ ├── N_P_Glyma.11G141800.Wm82.a2.v1_litre.jpg │ ├── N_P_Glyma.13G173100.Wm82.a2.v1_litre.jpg │ ├── N_P_Glyma.13G293500.Wm82.a2.v1_litre.jpg │ ├── N_P_Glyma.19G168700.Wm82.a2.v1_litre.jpg │ ├── bigPint.html │ ├── convertSEPair.html │ ├── convertSESubsetGenes.html │ ├── figures │ │ ├── lkClusters.png │ │ ├── lkSM2.png │ │ ├── logo.png │ │ ├── sbIRStreak2.png │ │ └── yeastWithinBetween.png │ ├── index.html │ ├── plotClusters-1.png │ ├── plotClusters-2.png │ ├── plotClusters-3.png │ ├── plotClusters-4.png │ ├── plotClusters-5.png │ ├── plotClusters.html │ ├── plotLitre-1.png │ ├── plotLitre-2.png │ ├── plotLitre-3.png │ ├── plotLitre.html │ ├── plotLitreApp.html │ ├── plotPCP-1.png │ ├── plotPCP-2.png │ ├── plotPCP-3.png │ ├── plotPCP.html │ ├── plotPCPApp.html │ ├── plotSM-1.png │ ├── plotSM-2.png │ ├── plotSM-3.png │ ├── plotSM-4.png │ ├── plotSM-5.png │ ├── plotSM-6.png │ ├── plotSM-7.png │ ├── plotSM-8.png │ ├── plotSM.html │ ├── plotSMApp.html │ ├── plotVolcano-1.png │ ├── plotVolcano-2.png │ ├── plotVolcano-3.png │ ├── plotVolcano.html │ ├── plotVolcanoApp.html │ ├── se_soybean_cn_sub.html │ ├── se_soybean_ir_sub.html │ ├── soybean_cn.html │ ├── soybean_cn_metrics.html │ ├── soybean_cn_sub.html │ ├── soybean_cn_sub_metrics.html │ ├── soybean_ir.html │ ├── soybean_ir_metrics.html │ ├── soybean_ir_sub.html │ └── soybean_ir_sub_metrics.html └── sitemap.xml ├── index.html ├── index.md ├── inst ├── .DS_Store~ ├── CITATION ├── shiny-dashboards │ ├── litre │ │ ├── app.R │ │ ├── rsconnect │ │ │ └── shinyapps.io │ │ │ │ └── bigpint │ │ │ │ └── litre.dcf │ │ ├── soybean_ir_sub.rda │ │ ├── soybean_ir_sub_metrics.rda │ │ └── www │ │ │ ├── Figure1.png │ │ │ ├── Figure2.png │ │ │ ├── Figure3.png │ │ │ └── Figure4.png │ ├── litrePresentation │ │ ├── add1_metrics.rda │ │ ├── app.R │ │ ├── kidneyLiver.rda │ │ ├── rsconnect │ │ │ └── shinyapps.io │ │ │ │ └── bigpint │ │ │ │ ├── litre.dcf │ │ │ │ └── litrePresentation.dcf │ │ ├── soybean_ir_sub.rda │ │ ├── soybean_ir_sub_metrics.rda │ │ └── www │ │ │ ├── Figure1.png │ │ │ ├── Figure2.png │ │ │ ├── Figure3.png │ │ │ └── Figure4.png │ ├── pcplot │ │ ├── app.R │ │ ├── rsconnect │ │ │ └── shinyapps.io │ │ │ │ └── bigpint │ │ │ │ └── pcplot.dcf │ │ ├── soybean_ir_sub.rda │ │ ├── soybean_ir_sub_metrics.rda │ │ └── www │ │ │ ├── .DS_Store~ │ │ │ ├── Figure1.png │ │ │ ├── Figure2.png │ │ │ ├── Figure3.png │ │ │ └── Figure4.png │ ├── smplot │ │ ├── rsconnect │ │ │ └── shinyapps.io │ │ │ │ └── bigpint │ │ │ │ └── smplot.dcf │ │ ├── server.R │ │ ├── soybean_cn_sub.rda │ │ ├── ui.R │ │ └── www │ │ │ ├── .DS_Store~ │ │ │ ├── Figure1.png │ │ │ ├── Figure2.png │ │ │ ├── Figure3.png │ │ │ └── Figure4.png │ └── volcano │ │ ├── app.R │ │ ├── rsconnect │ │ └── shinyapps.io │ │ │ └── bigpint │ │ │ └── volcano.dcf │ │ ├── soybean_ir_sub.rda │ │ ├── soybean_ir_sub_metrics.rda │ │ └── www │ │ ├── .DS_Store~ │ │ ├── Figure1.png │ │ ├── Figure2.png │ │ ├── Figure3.png │ │ └── Figure4.png ├── shiny-examples │ ├── .DS_Store~ │ ├── plotLitreApp │ │ ├── .DS_Store~ │ │ ├── app.R │ │ └── www │ │ │ ├── .DS_Store~ │ │ │ ├── Figure1.png │ │ │ ├── Figure2.png │ │ │ ├── Figure3.png │ │ │ └── Figure4.png │ ├── plotPCPApp │ │ ├── .DS_Store~ │ │ ├── app.R │ │ ├── logs │ │ │ └── shinylogs_plotPCPApp_1581655461437265000.json │ │ └── www │ │ │ ├── .DS_Store~ │ │ │ ├── Figure1.png │ │ │ ├── Figure2.png │ │ │ ├── Figure3.png │ │ │ └── Figure4.png │ ├── plotSMApp │ │ ├── .DS_Store~ │ │ ├── app.R │ │ ├── logs │ │ │ └── shinylogs_plotSMApp_1580880279969655000.json │ │ ├── manifest.json │ │ └── www │ │ │ ├── .DS_Store~ │ │ │ ├── Figure1.png │ │ │ ├── Figure2.png │ │ │ ├── Figure3.png │ │ │ └── Figure4.png │ └── plotVolcanoApp │ │ ├── .DS_Store~ │ │ ├── app.R │ │ └── www │ │ ├── .DS_Store~ │ │ ├── Figure1.png │ │ ├── Figure2.png │ │ ├── Figure3.png │ │ └── Figure4.png └── unitTests │ ├── test_data.R │ ├── test_dataMetrics.R │ ├── test_dataMetricsLitreApp.R │ ├── test_dataMetricsVolcano.R │ └── test_dataMetricsVolcanoApp.R ├── man ├── bigPint.Rd ├── convertSEPair.Rd ├── convertSESubsetGenes.Rd ├── figures │ ├── lkClusters.png │ ├── lkSM2.png │ ├── logo.png │ ├── sbIRStreak2.png │ └── yeastWithinBetween.png ├── plotClusters.Rd ├── plotLitre.Rd ├── plotLitreApp.Rd ├── plotPCP.Rd ├── plotPCPApp.Rd ├── plotSM.Rd ├── plotSMApp.Rd ├── plotVolcano.Rd ├── plotVolcanoApp.Rd ├── se_soybean_cn_sub.Rd ├── se_soybean_ir_sub.Rd ├── 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