Make QTHist consistent

now QThist will show percentages, rather then frequencies,
for single distributions as well as multi-distributions.
Also, the numbers param now works in both cases. Fix #179

Author: nsheff

R/feature-plots.R

@@ -17,7 +17,7 @@
 # @return A vector of genomic distances for each query region relative to its 
 #         closest feature.
 calcFeatureDistBioc = function(query, features) {
-    .validateInputs(list(query=x("GRangesList","GRanges")))
+    .validateInputs(list(query=c("GRangesList","GRanges")))
     if (is(query, "GRangesList")) {
         # Recurse over each GRanges object
         x = lapply(query, calcFeatureDist, features)
@@ -337,6 +337,7 @@ cutDists = function(dists, divisions=NULL, nbins=50,
     labels = labelCuts(sort(divisions), collapse=" to ", infBins=infBins)
     cuts = cut(dists, divisions, labels)
     df = as.data.frame(table(cuts))
+    setDT(df)
     return(df)
 }
 

R/qthist.R

@@ -90,6 +90,8 @@ plotQTHist = function(x, EndBarColor = "gray57", MiddleBarColor = "gray27",
         g = ggplot(df, aes(x=cuts, y=Freq, fill=name)) + 
             facet_wrap(. ~name)
     } else {
+        if (!numbers)
+            df$Freq = df[, .(Freq.Per = (Freq / sum(Freq)) * 100)]$"Freq.Per"
         g = ggplot(df, aes(x=cuts, y=Freq))
     }
     # Create a vector for the colors
@@ -114,6 +116,10 @@ plotQTHist = function(x, EndBarColor = "gray57", MiddleBarColor = "gray27",
         theme(legend.position="bottom") +
         geom_text(aes(label= paste((output[["quantile"]]*100),"%", sep='')),
             data=df[qbaridx,], hjust=-1, angle=90, size=2.5)
+
+    if (!numbers)
+        g = g + ylab("Percentage")
+    
     return(g)
 }