Init

.Rbuildignore

@@ -0,0 +1,9 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^data-raw$
+^dev$
+$run_dev.*
+^README\.Rmd$
+^docs$
+^media$
+^pkgdown$

.gitattributes

@@ -0,0 +1,2 @@
+*.html linguist-vendored
+*.css linguist-vendored

.gitignore

@@ -1,3 +1,22 @@
+pkgdown
+vignettes/info
+dev/
+inst/shiny/
+inst/shiny/data/
+data-raw/
+/docs/
+*.psd
+*.ai
+*.svg
+
+# App keys
+*.Rproj
+.Renviron
+
+# Packrat lockfiles generated during RSC deploy
+packrat.lock
+rsconnect/
+
 # History files
 .Rhistory
 .Rapp.history
@@ -20,10 +39,6 @@
 # RStudio files
 .Rproj.user/
 
-# produced vignettes
-vignettes/*.html
-vignettes/*.pdf
-
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
 
@@ -35,5 +50,32 @@ vignettes/*.pdf
 *.utf8.md
 *.knit.md
 
-# R Environment Variables
-.Renviron
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+.Rproj.user
+*.yml
+inst/script/data/yeast-tfs.csv

DESCRIPTION

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+Package: bieulergy
+Title: Interactive analysis of multi-omics regulatory networks
+Version: 1.0.0
+Authors@R: c(person(given="Anthony", family="Federico", email="[email protected]", 
+             role=c("aut", "cre")),
+             person(given="Stefano", family="Monti", email="[email protected]", 
+             role=c("aut")))
+Description: Graph-theoretic approaches for the analysis and visualization of multi-omics regulatory networks.
+Depends: R (>= 4.0.0)
+License: GPL-3 + file LICENSE
+URL: https://github.com/montilab/bieulergy
+Imports: 
+    config,
+    shiny,
+    htmltools,
+    rjson,
+    httr,
+    R6,
+    scales,
+    ggplot2,
+    ggrepel,
+    ggpubr,
+    reshape2,
+    viridis,
+    dplyr,
+    plyr,
+    tidyr,
+    tibble,
+    stringr,
+    magrittr,
+    dnet,
+    glue,
+    igraph,
+    centiserve,
+    sna,
+    visNetwork,
+    FactoMineR,
+    factoextra
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.1.1
+Suggests: 
+    shinyjs,
+    shinythemes,
+    testthat,
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr

Dockerfile

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+FROM rocker/tidyverse:4.0.0-ubuntu18.04
+
+COPY . /bieulergy
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    apt-utils \
+    libglpk-dev \
+    libcurl4-openssl-dev \
+    libxml2-dev \
+    libssl-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN Rscript -e "devtools::install('bieulergy', dependencies=TRUE)"

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(cfx)
+export(colorize)
+export(colorize.heat)
+export(create.ionet)
+export(create.ionets)
+export(ggempty)
+export(ggeplot)
+export(ggwrs)
+export(ig.assortivity)
+export(ig.betweeness)
+export(ig.centrality)
+export(ig.clustering)
+export(ig.components)
+export(ig.create)
+export(ig.dangalchev)
+export(ig.degree)
+export(ig.density)
+export(ig.diameter)
+export(ig.diffusion)
+export(ig.eccentricity)
+export(ig.edges)
+export(ig.efficiency)
+export(ig.eigen)
+export(ig.isolated)
+export(ig.katz)
+export(ig.laplacian)
+export(ig.leverage)
+export(ig.nodes)
+export(ig.properties)
+export(ig.rwr)
+export(ig.stress)
+export(ig.to.vn)
+export(ig.topoco)
+export(ig.transitivity)
+export(interactive.omics.network)
+export(is.ionet)
+export(is.network)
+export(is.networks)
+export(kstest)
+export(network.kstest)
+export(network.pca.contri)
+export(network.pca.hclust)
+export(network.pca.pltvar)
+export(network.pca.varexp)
+export(networks.cdistr)
+export(networks.diffc)
+export(networks.hclust)
+export(networks.tnodes)
+export(normalize.nlog)
+export(normalize.nlog.range)
+export(normalize.range)
+export(normalize.zo)
+export(pseudo.log.trans)
+export(pseudo.log.trans.rev)
+export(rcolors)
+export(run.shiny)
+export(theme_simplex)
+export(vn.to.ig)
+import(viridis)
+importFrom(FactoMineR,PCA)
+importFrom(R6,R6Class)
+importFrom(centiserve,closeness.residual)
+importFrom(centiserve,diffusion.degree)
+importFrom(centiserve,katzcent)
+importFrom(centiserve,laplacian)
+importFrom(centiserve,leverage)
+importFrom(centiserve,topocoefficient)
+importFrom(dnet,dRWR)
+importFrom(dplyr,arrange)
+importFrom(dplyr,bind_cols)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,desc)
+importFrom(dplyr,filter)
+importFrom(dplyr,if_else)
+importFrom(dplyr,mutate)
+importFrom(dplyr,pull)
+importFrom(dplyr,select)
+importFrom(dplyr,sym)
+importFrom(factoextra,fviz_contrib)
+importFrom(factoextra,fviz_dend)
+importFrom(factoextra,fviz_pca_var)
+importFrom(factoextra,fviz_screeplot)
+importFrom(factoextra,get_dist)
+importFrom(factoextra,hcut)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,annotate)
+importFrom(ggplot2,coord_flip)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_rect)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_hline)
+importFrom(ggplot2,geom_jitter)
+importFrom(ggplot2,geom_rug)
+importFrom(ggplot2,geom_text)
+importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,geom_vline)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,qplot)
+importFrom(ggplot2,scale_colour_manual)
+importFrom(ggplot2,scale_fill_gradient)
+importFrom(ggplot2,scale_y_continuous)
+importFrom(ggplot2,scale_y_reverse)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_bw)
+importFrom(ggplot2,theme_classic)
+importFrom(ggplot2,theme_void)
+importFrom(ggplot2,xlab)
+importFrom(ggplot2,ylab)
+importFrom(ggpubr,ggarrange)
+importFrom(ggpubr,ggboxplot)
+importFrom(ggpubr,ggdensity)
+importFrom(ggpubr,ggecdf)
+importFrom(ggpubr,ggscatter)
+importFrom(ggpubr,stat_compare_means)
+importFrom(ggrepel,geom_label_repel)
+importFrom(glue,glue)
+importFrom(grDevices,colorRampPalette)
+importFrom(igraph,V)
+importFrom(igraph,as_adjacency_matrix)
+importFrom(igraph,as_ids)
+importFrom(igraph,assortativity_degree)
+importFrom(igraph,count_components)
+importFrom(igraph,degree)
+importFrom(igraph,delete_edge_attr)
+importFrom(igraph,diameter)
+importFrom(igraph,distances)
+importFrom(igraph,eccentricity)
+importFrom(igraph,ecount)
+importFrom(igraph,eigen_centrality)
+importFrom(igraph,graph_from_adjacency_matrix)
+importFrom(igraph,graph_from_data_frame)
+importFrom(igraph,is_simple)
+importFrom(igraph,simplify)
+importFrom(igraph,transitivity)
+importFrom(igraph,vcount)
+importFrom(magrittr,"%>%")
+importFrom(magrittr,set_colnames)
+importFrom(magrittr,set_names)
+importFrom(plyr,rbind.fill)
+importFrom(reshape2,melt)
+importFrom(scales,trans_new)
+importFrom(shiny,runApp)
+importFrom(sna,betweenness)
+importFrom(sna,stresscent)
+importFrom(stringr,str_to_title)
+importFrom(tibble,deframe)
+importFrom(tidyr,drop_na)
+importFrom(visNetwork,toVisNetworkData)
+importFrom(visNetwork,visEdges)
+importFrom(visNetwork,visIgraphLayout)
+importFrom(visNetwork,visNetwork)
+importFrom(visNetwork,visNodes)

R/app.R

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+#' Spin up an instance of the shiny application
+#'
+#' @param launch.browser Launch in browser mode
+#' @param dev Refresh server upon code changes
+#' 
+#' @importFrom shiny runApp
+#'
+#' @export
+run.shiny <- function(launch.browser=TRUE, dev=TRUE) {
+    app.dir <- system.file("shiny", package="bieulergy")
+    if (dev) options(shiny.autoreload=TRUE)
+    shiny::runApp(app.dir, launch.browser=launch.browser, display.mode="normal")
+}