annotate barplot.r @ 6:8829656d6999 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"

if (length(commandArgs(TRUE)) == 0) {
  system("Rscript barplot.r -h", intern = F)
  q("no")
}


# load packages that are provided in the conda env
options( show.error.messages=F,
       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
warnings()
library(optparse)
library(ggplot2)
library(ggrepel)
library(RColorBrewer)


#Arguments
option_list = list(
  make_option(
    c("-i", "--input"),
    default = NA,
    type = 'character',
    help = "Input file that contains count data (no header)"
  ),
  make_option(
    c("-o", "--barplot"),
    default = NA,
    type = 'character',
    help = "PDF output file"
  )
)

opt = parse_args(OptionParser(option_list = option_list),
                 args = commandArgs(trailingOnly = TRUE))


## 
annotations = read.delim(opt$input, header=F)
colnames(annotations) = c("sample", "class", "percent_of_reads", "total")
annotations$percent=round(annotations$percent_of_reads/annotations$total*100, digits=2)
# ggplot2 plotting

# Define the number of colors you want
Sasha.Trubetskoy.Palette <- c('#e6194b', '#3cb44b', '#ffe119', '#4363d8', '#f58231',
                              '#911eb4', '#46f0f0', '#f032e6', '#bcf60c',
                              '#008080', '#e6beff', '#9a6324', '#fffac8', '#800000',
                              '#aaffc3', '#808000', '#ffd8b1', '#000075', '#808080')
nb.cols <- 19  # 10 with colorRampPalette
# mycolors <- colorRampPalette(brewer.pal(8, "Paired"))(nb.cols)
mycolors <- Sasha.Trubetskoy.Palette[1:nb.cols]

ggtitle('Class proportions') 
ggplot(annotations, aes(x=total/2, y = percent_of_reads, fill = class, width = total)) +
       geom_bar(position="fill", stat="identity") + 
       facet_wrap(~sample, ncol=3 ) +
       geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5), size=2,show.legend = F) +
       coord_polar(theta="y") +
       labs(x = "Class fractions (%)") +
       scale_fill_manual(values = mycolors) +
       theme(axis.text = element_blank(),
             axis.ticks = element_blank(),
             panel.grid  = element_blank(),
             axis.title.y = element_blank(),
             legend.position="bottom") +
       geom_text(aes(x = total/2, y= .5, label = paste(round(total/1000000, digits=3), "M"), vjust = 4, hjust=-1), size=2)
ggsave(file=opt$barplot, device="pdf")