Re-add deleted files - bouhhh Stevenn

META16S_App.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

google-analytics.js

+  (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
+  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
+  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
+  })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
+
+  ga('create', 'UA-72614324-2', 'auto');
+  ga('send', 'pageview');

libraries_updates.R

+#### to avoid conflict between d3heatmap and rnvd3 #####
+# the conflict come from the fact that both libraries use d3 but not the same version
+# when the most recent one is loaded (the one of d3heatmap), it breaks the one of rNVD3
+# the idea here is to modify the d3 of d3heatmap so that the library create an object called d33
+# then modify the d3heatmap files so that it use this d33 object instead of d3
+
+# first get d3heatmap javascript library path
+d3heatmap_path = paste(.libPaths(), 'd3heatmap/htmlwidgets/lib/', sep='/')
+
+# then get all js files in this directory
+js_files = dir(path=d3heatmap_path, pattern = "*.js$", recursive = T, full.names = T)
+
+# then create a function tu update the files
+d3_to_d33 = function(target){
+  # the function will use the bash tool sed on the file target
+  # it makes 3 replacements
+  system(command=paste('sed -i .bck -e "s/d3\\ /d33 /g" -e "s/d3\\./d33./g" -e "s/d3;/d33;/g" ', target))
+}
+# apply the replacement function to all js files
+sapply(js_files, d3_to_d33)
+
+# change from d3.min.js to d3.js in the yaml file
+system(command=paste('sed -i .bck -e "s/d3\\.min/d3/g" ', .libPaths(), '/d3heatmap/htmlwidgets/d3heatmap.yaml', sep=''))
+
+# it's done. d3heatmap should use d33 object now
+
+#### replacement of the css cals of the rNVD3 ####
+
+# get the rNVD3 path
+rNVD3_path = paste(.libPaths(), 'rNVD3/nvd3/css/', sep='/')
+
+# get the path of the current source. may need to be modified (parent.frame(1) or parent.frame(2) or parent.frame(3) or else) 
+current_path = dirname(parent.frame(2)$ofile) 
+# get the css files path
+css_files = dir(path=current_path, pattern = "*.css$", full.names = T)
+# create the function to copy the css file
+cp_to_rNVD3 = function(p, dest){
+  system(paste('cp', p, dest))
+}
+#apply the copy to all the css files
+sapply(css_files, cp_to_rNVD3, rNVD3_path)
+
+# first get d3heatmap javascript library path
+scatterD3_path = paste(.libPaths(), 'scatterD3/htmlwidgets/', sep='/')
+
+# then get all js files in this directory
+js_files = dir(path=scatterD3_path, pattern = "*.js$", recursive = T, full.names = T)
+
+# then create a function tu update the files
+d3_to_d333 = function(target){
+  # the function will use the bash tool sed on the file target
+  # it makes 3 replacements
+  system(command=paste('sed -i .bck -e "s/d3\\ /d333 /g" -e "s/d3\\./d333./g" -e "s/d3;/d333;/g" -e "s/d3=/d333=/g" ', target))
+}
+# apply the replacement function to all js files
+sapply(js_files, d3_to_d333)
+
+# change from d3.min.js to d3.js in the yaml file
+system(command=paste('sed -i .bck -e "s/d3$/d333/g" ', .libPaths(), '/scatterD3/htmlwidgets/scatterD3.yaml', sep=''))
+

r_packages_shaman.R

+if (!require("Rcpp")){
+  install.packages("Rcpp")
+}
+
+if(!require(shinydashboard)){
+  install.packages('shinydashboard')
+  library(shinydashboard)
+}
+
+if(!require(rjson)){
+  install.packages('rjson')
+}
+
+if(!require(devtools)){
+  install.packages('devtools')
+}
+
+if (!require(psych)) {
+  install.packages('psych')
+  library(psych)
+}
+
+if (!require(ggplot2)) {
+  install.packages('ggplot2')
+  library(ggplot2)
+}
+if (!require(vegan)) {
+  install.packages('vegan')
+  library(vegan)
+}
+
+if (!require(dendextend)) {
+  install.packages('dendextend')
+  library(dendextend)
+}
+
+if (!require(circlize)) {
+  install.packages('circlize')
+  library(circlize)
+}
+
+if (!require(d3heatmap)) {
+  install.packages('d3heatmap')
+  library(d3heatmap)
+}
+
+if (!require(biom)) {
+  install.packages('biom')
+  library(biom)
+}
+
+if (!require(devtools)) {
+  install.packages('devtools')
+  library(devtools)
+}
+
+if (!require(scatterD3)) {
+  install.packages('scatterD3')
+  library(scatterD3)
+}
+
+if (!require(rNVD3)) {
+  library(devtools)
+  install_github('rNVD3', 'ramnathv')
+  library(rNVD3)
+}
+
+if (!require(genefilter)) {
+  source("https://bioconductor.org/biocLite.R")
+  biocLite("genefilter")
+  library(genefilter)
+}
+
+if (!require(googleVis)) {
+  install.packages('googleVis')
+  suppressPackageStartupMessages(library(googleVis))
+}
+
+if (!require(shinyjs)) {
+  install.packages('shinyjs')
+  library(shinyjs)
+}
+
+if (!require(psych)) {
+  install.packages('psych')
+  library(psych)
+}
+
+if (!require(ggplot2)) {
+  install.packages('ggplot2')
+  library(ggplot2)
+}
+
+if (!require(vegan)) {
+  install.packages('vegan')
+  library(vegan)
+}
+
+if (!require(dendextend)) {
+  install.packages('dendextend')
+  library(dendextend)
+}
+
+if (!require(circlize)) {
+  install.packages('circlize')
+  library(circlize)
+}
+
+if (!require(biom)) {
+  install.packages('biom')
+  library(biom)
+}
+
+if (!require(DT)) {
+  install.packages('DT')
+  library(DT)
+}
+
+if (!require(RColorBrewer)) {
+  install.packages('RColorBrewer')
+  library(RColorBrewer)
+}
+
+if (!require(scatterD3)) {
+  install.packages('scatterD3')
+  library(scatterD3)
+}
+
+if (!require(gplots)) {
+  install.packages('gplots')
+  library(gplots)
+}
+
+if (!require(DESeq2)) {
+  source("https://bioconductor.org/biocLite.R")
+  biocLite("DESeq2")
+  library(DESeq2)
+}
+
+if (!require(ade4)) {
+  install.packages('ade4')
+  library(ade4)
+}
+
+if (!require(genefilter)) {
+  source("https://bioconductor.org/biocLite.R")
+  biocLite("genefilter")
+  library(genefilter)
+}
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