--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/size_histogram.r	Tue Jul 11 11:44:36 2017 -0400
@@ -0,0 +1,110 @@
+## Setup R error handling to go to stderr
+options( show.error.messages=F,
+         error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+library(RColorBrewer)
+library(lattice)
+library(latticeExtra)
+library(grid)
+library(gridExtra)
+library(optparse)
+
+# Parse arguments
+option_list <- list(
+    make_option(c("-g", "--global"), type="character", help="Whether distribution is plotted globally or by chromosome"),
+    make_option(c("-s", "--size_distribution_tab"), type="character", help="Path to file with tabular size distribution"),
+    make_option("--size_distribution_pdf", type="character", help="Path to file with size distribution plot"),
+    make_option("--title", type="character", help="Title for readmaps and size distribution"),
+    make_option("--ylabel", type="character", help="ylabel for readmaps and size distribution"),
+    make_option("--yrange", type="integer", help="Y-axis range"),
+    make_option("--rows_per_page", type="integer", help="rows_per_page")
+    )
+
+parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
+args = parse_args(parser)
+
+##cheetahtemplate data frame implementation
+size=read.delim(args$size_distribution_tab, header=T, row.names=NULL)
+n_samples = length(unique (size$sample))
+n_genes = length (unique (levels(size$gene)))
+
+if (args$yrange != 0) {
+   # This is used for specifying the y-axis limits
+   ylim=c(-args$yrange, args$yrange)
+} else { ylim="" }
+
+par.settings.size=list(layout.heights=list(top.padding=1, bottom.padding=1),
+                       strip.background = list(col = c("lightblue", "lightgreen"))
+                       )
+
+smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);} # use if one want y axis in the middle of the plot
+
+plot_size_distribution = function(df, ...) {
+   bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0,
+                horizontal=FALSE,
+            group=polarity,
+            stack=TRUE,
+                col=c('red', 'blue'),
+                cex=0.75,
+                scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.5, alternating=T), x=list(cex=.6 ) ),
+                xlab = "readsize in nucleotides",
+                ylab = args$ylabel,
+                main = args$title,
+                par.strip.text = list(cex=0.75),
+                as.table=TRUE,
+                newpage = T,
+                ...)
+
+    combineLimits(update(useOuterStrips(bc,
+                                        strip.left = strip.custom(par.strip.text = list(cex=0.5))
+                                        ),
+                  layout=c(n_samples,args$rows_per_page)),
+                  margin.x=F, margin.y=1)
+    }
+
+# per_gene_size=lapply(genes, function(x) subset(size, gene==x)) # no object in this script
+
+if (args$global == "no") {
+width = 8.2677*n_samples/4
+} else { width = 8.2677 }
+
+options(warn=-1)
+pdf(file=args$size_distribution_pdf, paper="special", height=11.69, width=width)
+
+if (ylim == "" && args$global=="no") {
+    plot_size_distribution(size, par.settings=par.settings.size)
+   }
+if (ylim != "" && args$global=="no") { plot_size_distribution(size, par.settings=par.settings.size, ylim=ylim)
+   }
+if (ylim == "" && args$global=="yes") {  bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample)),
+        data = size, origin = 0,
+        horizontal=FALSE,
+        group=polarity,
+        stack=TRUE,
+        col=c('red', 'blue'),
+        scales=list(y=list(tick.number=4, rot=90, relation="same"), cex=1),
+        xlab = "readsize in nucleotides",
+        ylab = args$ylabel,
+        main = args$title, as.table=TRUE, newpage = T,
+        aspect=0.5,
+        strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue")
+        )
+   bc
+   }
+if (ylim != "" && args$global=="yes") {  bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample)),
+        data = size, origin = 0,
+        horizontal=FALSE,
+        group=polarity,
+        stack=TRUE,
+        col=c('red', 'blue'),
+        scales=list(y=list(tick.number=4, rot=90, relation="same"), cex=1),
+        xlab = "readsize in nucleotides",
+        ylab = args$ylabel,
+        ylim = ylim,
+        main = args$title, as.table=TRUE, newpage = T,
+        aspect=0.5,
+        strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue")
+        )
+   bc
+   }
+
+devname=dev.off()