tRAX/genefeatures.R at master · UCSC-LoweLab/tRAX · GitHub

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#library(ggsci)
library(ggplot2)
library(reshape2)
library(scales)
library(RColorBrewer)

args <- commandArgs(trailingOnly = TRUE)


counts <- read.table(args[1],check.names=FALSE)

selectcounts = counts


temp = cbind(selectcounts, seq = factor(rownames(selectcounts),rev(rownames(selectcounts)), ordered = TRUE))


countsmelt = melt(temp, id.vars = c('seq'))


countsmelt = within(countsmelt, seq <- factor(seq,
    rownames(selectcounts),
    ordered = FALSE))

sampletotals = aggregate(countsmelt$value, list(countsmelt$variable), sum)


#sampletotals$x[countsmelt$variable]
#countsmelt = countsmelt[countsmelt$value > 100,]
countsmelt = countsmelt[countsmelt$value > sampletotals$x[countsmelt$variable] / 100,]


#unique(countsmelt$seq)
colourCount = length(unique(countsmelt$seq))+1
#getPalette = colorRampPalette(brewer.pal(8, "Dark2"))
getPalette = colorRampPalette(brewer.pal(9, "Set1"))

#unique(head(countsmelt))

#   other #f2dab2
#   tRNA #6666cc
#   pretRNA #a1ade5
#   miRNA #b4008d
#   snRNA #74531d
#   Mt_tRNA #87e275
#   Mt_rRNA #00754a
#   rRNA    #a5e5d9
#   snoRNA  #ff9e18
#   misc_RNA    #b2b2b2

typepal <- c(
  "tRNA" = "#6666cc",
  "pretRNA" = "#a1ade5",
  "miRNA" = "#b4008d",
  "snRNA" = "#74531d",
  "Mt_tRNA" = "#87e275",
  "Mt_rRNA" = "#00754a",
  "rRNA" = "#a5e5d9",
  "snoRNA" = "#ff9e18",
  "misc_RNA" = "#b2b2b2",
  "other" = "#f2dab2"
)


#print(typepal)


#print(setdiff(unique(countsmelt$seq),names(typepal)))

extragenes = setdiff(unique(countsmelt$seq),names(typepal))

otherpal = getPalette(length(extragenes))

names(otherpal) = extragenes

#print(otherpal)

typepal = c(typepal, otherpal)

#print(typepal)

ggplot(countsmelt,aes(x = variable, y = value,fill = seq, stat="identity")) + theme_bw() + theme(panel.border = element_rect(linetype = "blank"), panel.grid = element_line(linetype = "blank")) +
	geom_bar(position = "fill",stat="identity") +
    geom_bar(position = "fill",stat="identity",color="black",show.legend=FALSE) +
    scale_y_continuous(labels = percent_format()) +
    theme(axis.text.x = element_text(size=5))+
    xlab("Sample") +
    ylab("Percentage of Total Reads") +
    labs(fill="Read\nType")+
    #scale_fill_ucscgb()+
    #scale_fill_brewer(palette = "Dark2")+
    #scale_fill_manual(values = getPalette(colourCount))+
    scale_fill_manual(values = typepal)+
    theme(axis.title.x = element_text(face="bold", size=15), axis.text.x = element_text(face="bold", size=9,angle = 90, vjust = .5)) #+scale_colour_gradient() #+ scale_fill_brewer( palette="RdPu")

ggsave(filename=args[2])