Code cleaning and add shamanapp

libraries_updates.R

@@ -27,18 +27,18 @@ system(command=paste('sed -i .bck -e "s/d3\\.min/d3/g" ', .libPaths(), '/d3heatm
 #### replacement of the css cals of the rNVD3 ####
 
 # get the rNVD3 path
-rNVD3_path = paste(.libPaths(), 'rNVD3/nvd3/css/', sep='/')
+#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)$ofile) 
+#current_path = dirname(parent.frame(2)$ofile) 
 # get the css files path
-css_files = dir(path=current_path, pattern = "*.css$", full.names = T)
+#css_files = dir(path=current_path, pattern = "*.css$", full.names = T)
 # create the function to copy the css file
-cp_to_rNVD3 = function(p, dest){
-  system(paste('cp', p, dest))
-}
+#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)
+#sapply(css_files, cp_to_rNVD3, rNVD3_path)
 
 # first get d3heatmap javascript library path
 scatterD3_path = paste(.libPaths(), 'scatterD3/htmlwidgets/', sep='/')

www/base/BaseContrast_144854511.txt

-"WT_0_6" "Delta_0_6" "DeltaCompl_0_6" "Delta_DeltaCompl_0_6" "WT_0_24" "Delta_0_24" "DeltaCompl_0_24" "Delta_DCompl_0_24" "Delta_WT_0_24" "Dcompl_WT_0_6" "Dcompl_WT_0_24"
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
--1 -1 -1 0 -1 -1 -1 0 0 0 0
-1 1 1 0 0 0 0 0 0 0 0
-0 0 0 0 1 1 1 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 -1 0 -1 0 -1 0 -1 -1 0 0
-0 0 -1 1 0 0 -1 1 0 -1 -1
--1 0 0 0 -1 0 0 0 1 1 1
-0 1 0 1 0 0 0 0 0 0 0
-0 0 1 -1 0 0 0 0 0 1 0
-1 0 0 0 0 0 0 0 0 -1 0
-0 0 0 0 0 1 0 1 1 0 0
-0 0 0 0 0 0 1 -1 0 0 1
-0 0 0 0 1 0 0 0 -1 0 -1

www/base/BaseContrast_150596656.txt

-"WT_0_6" "Delta_0_6" "DeltaCompl_0_6" "Delta_DeltaCompl_0_6" "Delta_WT_0_6" "WT_0_24" "Delta_0_24" "DeltaCompl_0_24" "Delta_DCompl_0_24" "Delta_WT_0_24" "Contrast name"
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
--1 -1 -1 0 0 -1 -1 -1 0 0 0
-1 1 1 0 0 0 0 0 0 0 0
-0 0 0 0 0 1 1 1 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0 0
-0 -1 0 -1 -1 0 -1 0 -1 -1 0
-0 0 -1 1 0 0 0 -1 1 0 0
--1 0 0 0 1 -1 0 0 0 1 0
-0 1 0 1 1 0 0 0 0 0 0
-0 0 1 -1 0 0 0 0 0 0 0
-1 0 0 0 -1 0 0 0 0 0 0
-0 0 0 0 0 0 1 0 1 1 0
-0 0 0 0 0 0 0 1 -1 0 0
-0 0 0 0 0 1 0 0 0 -1 0

www/base/BaseContrast_171123185.txt

-"Name..." "Name....1" "Name..."
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0
-0 0 0