--- a
+++ b/R/addons.R
@@ -0,0 +1,102 @@
+###########################################################
+### ADDITIONAL FUNCTIONS
+###########################################################
+
+# Wide to long format conversion
+meltWholeDF = function(df) {
+  data.frame(X=rep(colnames(df), each=nrow(df)),
+             Y=rep(rownames(df), times=ncol(df)),
+             Measure=as.vector(as.matrix(df)))
+}
+
+# Smart unlist - preserves the names of the vectors as they were
+smunlist = function(li) {
+  setNames(unlist(li),
+           nm=unname(rapply(li,
+                            function(i)
+                              if(!is.null(names(i)))
+                                names(i)
+                            else
+                              rep("", length(i)))))
+}
+
+# Function that gives nice drug names out of IDs (D_001-40 or D_001_5 type)
+giveDrugLabel = function(drid, ctab, dtab) {
+  vapply(strsplit(drid, "-"), function(x) {
+    if(length(x)==2) { # ID type: D_001-40
+      paste0(dtab[x[1],"name"], " ", x[2], " \u00B5", "M")
+    } else if(length(x)==1) { # ID type: D_001_5
+      x = unlist(strsplit(drid, "_"))
+      k = paste(x[1:2], collapse="_")
+      paste0(dtab[k, "name"], " ", ctab[k, as.integer(x[3])], " \u00B5","M")
+    }}, character(1))
+}
+
+# Round up to the nearest 5
+moround = function(x,base) {
+    base*ceiling(x/base)
+}
+
+# capitalize the first letter
+toCaps = function(word) {
+  paste0(toupper(substring(word,1,1)), substring(word,2,nchar(word)))
+}
+
+# out of IDs likes D_001_1, strip the trailing '_1'
+stripConc <- function(x) 
+  vapply(strsplit(x, "_"), function(x)
+    paste(x[-length(x)], collapse="_"), character(1))
+
+# treshold an array from below and above
+deckel <- function(x, lower = -Inf, upper = +Inf)
+  ifelse(x<lower, lower, ifelse(x>upper, upper, x))
+
+# log10 scale labels in ggplot2, use: scale_x_log10(labels=scientific_10)
+scientific_10 = function(x) {
+    x = scientific_format()(x)
+    parse(text=ifelse(x=="1e+00", "1   ", gsub("1e", "10^", x)))
+}
+
+# labels of volcano x axis scale
+percentAxisScale = function(x) {
+  x*100
+}
+
+# Function which computes log10 and returns with the sign of the input value
+log10div = function(x) {
+    sign(x)*log10(abs(x))  
+}
+
+# Function for axis labels of p-values going in two directions
+# (sensitive/resistant)
+exp10div = function(x) {
+    x = -abs(x)
+    x = paste0("10^", x)
+    x = gsub("10^0", "1", x, fixed=TRUE)
+    parse(text=x)
+}
+
+# change color names to hex with alpha level
+col2hex = function(cols, alpha=1, names=NA) {
+  tmp = col2rgb(cols) 
+  max = 255
+  tmp = apply(tmp, 2, function(t)
+    rgb(red=t[1], green=t[2], blue=t[3], maxColorValue=max, alpha=alpha*max))
+  if (all(!is.na(names)) && length(names)==length(tmp))
+      tmp = setNames(tmp,nm=names)
+  tmp
+}
+
+# safe match
+safeMatch <- function(x, ...) {
+  rv <- match(x, ...)
+  if (any(is.na(rv)))
+    stop(sprintf("`match` failed to match %s", paste(x[is.na(rv)],
+                                                     collapse=", ")))
+  rv 
+}
+
+# find out the index of appropriate layer in a grob table
+whichInGrob = function(grob, layer) {
+  match(layer, grob[["layout"]][["name"]])
+}
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