--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/small_rna_maps.r	Mon Jul 24 06:28:45 2017 -0400
@@ -0,0 +1,141 @@
+## Setup R error handling to go to stderr
+options( show.error.messages=F,
+       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+warnings()
+library(RColorBrewer)
+library(lattice)
+library(latticeExtra)
+library(grid)
+library(gridExtra)
+library(optparse)
+ 
+option_list <- list(
+    make_option(c("-r", "--output_tab"), type="character", help="path to tabular file"),
+    make_option(c("-s", "--sizes"), type="character", help="path to size dataframe"),
+    make_option("--output_pdf", type = "character", help="path to the pdf file with plot"),
+    make_option("--extra_plot", type = "character", help="what additional data should be plotted")
+    )
+ 
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
+args = parse_args(parser)
+if (length(args$sizes) != 0) { args$extra_plot <- "SizeDistribution"}
+ 
+# dataset manipulation
+
+Table = read.delim(args$output_tab, header=T, row.names=NULL)
+Table <- within(Table, Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
+n_samples=length(unique(Table$Dataset))
+genes=unique(levels(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)
+if (args$extra_plot == "SizeDistribution") {
+    size=read.delim(args$sizes, header=T, row.names=NULL)
+    size <- within(size, Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
+    per_gene_size=lapply(genes, function(x) subset(size, Chromosome==x))
+    }
+
+## end of data frames implementation
+
+## functions
+
+plot_readmap=function(df, ...) {
+    combineLimits(xyplot(Nbr_reads~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),
+    ...))
+    }
+
+
+plot_size=function(df, ...) {
+    #smR.prepanel=function(x,y,...) {; yscale=c(y*0, max(abs(y)));list(ylim=yscale);}
+    sizeplot = xyplot(eval(as.name(args$extra_plot))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
+    data=df,
+    type='p',
+    cex=0.35,
+    pch=19,
+    scales= list(relation="free", x=list(rot=0, cex=0, 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("darkred","darkblue"),
+    par.strip.text = list(cex=0.7),
+    ...)
+    combineLimits(sizeplot)
+    }
+
+plot_size_distribution= function(df, ...) {
+#  smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
+  bc= barchart(Nbr_reads~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, 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=0.7), x=list(cex=0.7) ),
+#    prepanel=smR.prepanel,
+    xlab = NULL,
+    ylab = NULL,
+    main = NULL,
+    as.table=TRUE,
+    newpage = T,
+    par.strip.text = list(cex=0.7),
+    ...)
+  combineLimits(bc)
+  }
+
+
+## end of functions
+
+## function parameters
+par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=0), strip.background = list(col=c("lightblue","lightgreen")) )
+par.settings.size=list(layout.heights=list(top.padding=0, bottom.padding=0))
+graph_title=list(Coverage="Read Maps and Coverages", Median="Read Maps and Median sizes", Mean="Read Maps and Mean sizes", SizeDistribution="Read Maps and Size Distributions")
+graph_legend=list(Coverage="Read counts / Coverage", Median="Read counts / Median size", Mean="Read counts / Mean size", SizeDistribution="Read counts")
+graph_bottom=list(Coverage="Nucleotide coordinates", Median="Nucleotide coordinates", Mean="Nucleotide coordinates", SizeDistribution="Read sizes / Nucleotide coordinates")
+## end of function parameters'
+
+## GRAPHS
+
+if (n_genes > 5) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=6} else {
+                 rows_per_page= n_genes; page_height_simple = 2.5*n_genes; page_height_combi=page_height_simple*2 }
+if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/2} # to test
+
+
+pdf(file=args$output_pdf, paper="special", height=page_height_simple, width=page_width)
+if (rows_per_page %% 2 != 0) { rows_per_page = rows_per_page + 1}
+for (i in seq(1,n_genes,rows_per_page/2)) {
+    start=i
+    end=i+rows_per_page/2-1
+    if (end>n_genes) {end=n_genes}
+    readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, strip=FALSE, par.settings=par.settings.readmap))
+    if (args$extra_plot == "SizeDistribution") {
+        size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, par.settings=par.settings.size))
+        }
+    else {
+        size_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_size(x, par.settings=par.settings.size))
+        }
+    
+        
+    plot.list=rbind(size_plot.list, readmap_plot.list)
+    args_list=c(plot.list, list(nrow=rows_per_page+1, ncol=1,
+                                    top=textGrob(graph_title[[args$extra_plot]], gp=gpar(cex=1), just="top"),
+                                    left=textGrob(graph_legend[[args$extra_plot]], gp=gpar(cex=1), vjust=1, rot=90),
+                                    sub=textGrob(graph_bottom[[args$extra_plot]], gp=gpar(cex=1), just="bottom")
+                                    )
+           )
+do.call(grid.arrange, args_list)
+}
+devname=dev.off()
+