--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/small_rna_clusters.r	Mon Oct 07 12:51:25 2019 -0400
@@ -0,0 +1,88 @@
+## Setup R error handling to go to stderr
+options( show.error.messages=F,
+         error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+options(warn = -1)
+library(RColorBrewer)
+library(lattice)
+library(latticeExtra)
+library(grid)
+library(gridExtra)
+library(optparse)
+
+option_list <- list(
+  make_option(c("-f", "--first_dataframe"), type="character", help="path to first dataframe"),
+  make_option("--first_plot_method", type = "character", help="How additional data should be plotted"),
+  make_option("--output_pdf", type = "character", help="path to the pdf file with plots")
+)
+
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
+args = parse_args(parser)
+
+# data frames implementation
+
+## first table
+Table = read.delim(args$first_dataframe, header=T, row.names=NULL)
+colnames(Table)[1] <- "Dataset"
+dropcol <- c("Strandness", "z.score") # not used by this Rscript and is dropped for backward compatibility
+Table <- Table[,!(names(Table) %in% dropcol)]
+if (args$first_plot_method == "Counts" | args$first_plot_method == "Size") {
+  Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
+}
+n_samples=length(unique(Table$Dataset))
+samples = unique(Table$Dataset)
+genes=unique(Table$Chromosome)
+per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x))
+per_gene_limit=lapply(genes, function(x) c(1, unique(subset(Table, Chromosome==x)$Chrom_length)) )
+n_genes=length(per_gene_readmap)
+
+## functions
+plot_unit = function(df, method=args$first_plot_method, ...) {
+    p = xyplot(Counts~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
+               data=df,
+               type='h',
+               lwd=1.5,
+               scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
+               xlab=NULL, main=NULL, ylab=NULL,
+               as.table=T,
+               origin = 0,
+               horizontal=FALSE,
+               group=Polarity,
+               col=c("red","blue"),
+               par.strip.text = list(cex=0.7),
+               ...)
+    p=combineLimits(p)
+}
+
+## function parameters
+par.settings.firstplot = list(layout.heights=list(top.padding=-2, bottom.padding=-2),strip.background=list(col=c("lightblue","lightgreen")))
+title_first_method = list(Counts="Read Counts", Coverage="Coverage depths", Median="Median sizes", Mean="Mean sizes", Size="Size Distributions")
+legend_first_method =list(Counts="Read count", Coverage="Coverage depth", Median="Median size", Mean="Mean size", Size="Read count")
+bottom_first_method =list(Counts="Coordinates (nucleotides)",Coverage="Coordinates (nucleotides)", Median="Coordinates (nucleotides)", Mean="Coordinates (nucleotides)", Size="Sizes of reads")
+
+## Plotting Functions
+single_plot <- function(...) {
+  width = 8.2677 * n_samples / 2
+  rows_per_page=8
+  graph_heights=c(rep(40,8),10)
+  pdf(file=args$output_pdf, paper="special", height=15, width=width)
+  for (i in seq(1,n_genes,rows_per_page)) {
+    start=i
+    end=i+rows_per_page-1
+    if (end>n_genes) {end=n_genes}
+    if (end-start+1 < 8) {graph_heights=c(rep(c(40),end-start+1),10,rep(c(40),8-(end-start+1)))}
+    first_plot.list = lapply(per_gene_readmap[start:end], function(x) update(useOuterStrips(plot_unit(x, par.settings=par.settings.firstplot),strip.left=strip.custom(par.strip.text = list(cex=0.5)))))
+    plot.list=rbind(first_plot.list)
+    args_list=c(plot.list, list( nrow=rows_per_page+1, ncol=1, heights=unit(graph_heights, rep("mm", 9)),
+                                 top=textGrob("Cluster Read Counts (Peaks in middle of clusters)", gp=gpar(cex=1), vjust=0, just="top"),
+                                 left=textGrob("Read Counts", gp=gpar(cex=1), vjust=0, hjust=0, x=1, y=(-0.41/7)*(end-start-(6.23/0.41)), rot=90),
+                                 sub=textGrob("Coordinates (nucleotides)", gp=gpar(cex=1), just="bottom", vjust=2)
+    )
+    )
+    do.call(grid.arrange, args_list)
+  }
+  devname=dev.off()
+}
+
+# main
+single_plot()
+