annotate coverage_plotting.R @ 15:ffcd42f85b61 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 5eb8570dce4e22fb2759cc16c8e1ce9d304508fe

#!/usr/bin/env Rscript

# Help to be printed
hlp_description <- "This script takes a dataframe containing the coverage values for different miRNAs and plots them."
hlp_usage <- "Usage : coverage_ploting.R --dataframe [FILE] --type ['relative' or 'absolute'] --output [FILE]"
hlp_dataframe <- "--dataframe\tFILE\tThis is a dataframe containing coverage values obtained from mircounts.py"
hlp_type <- "--type\t\tSTRING\tType of ploting, either relative or absoute coverage values (default='relative')"
hlp_output <- "--output\tFILE\tFile to output the pdf to\n"

hlp <- paste(hlp_description, hlp_usage, hlp_dataframe, hlp_type, hlp_output, sep = "\n")

# Setup R error handling to go to stderr
options(show.error.messages = FALSE,
    error = function() {
        cat(geterrmessage(), file = stderr())
        q("no", 1, FALSE)
    }
)

library(optparse)
library(lattice)

# Get arguments
option_list <- list(
    make_option(c("-d", "--dataframe"), type = "character",
                help = "Dataframe containing coverage values obtained from mircounts.py"),
    make_option(c("-t", "--type"), type = "character", default = "relative",
                help = "Type of plotting, either relative or absoute coverage values (default = 'relative')"),
    make_option(c("-o", "--output"), type = "character", help = "File to output the pdf to")
)
parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
args <- parse_args(parser)

if (!("dataframe" %in% names(args)) || !("output" %in% names(args))) {
    stop("'--dataframe' and '--output' parametters are not optional. Please retry.")
}

# Plot
coverage <- read.delim(args$dataframe, header = TRUE)
if (args$type == "relative") {
    graph <- xyplot(
        Norm_count ~ Norm_offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5,
        scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5),
        strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15),
        as.table = TRUE, xlab = "Normalized Counts", ylab = "Normalized coordinates",
        main = "miRNA coverage maps"
    )
} else {
    graph <- xyplot(
        Count ~ Offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5,
        scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5),
        strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15),
        as.table = TRUE, xlab = "Counts", ylab = "Coordinates",
        main = "miRNA coverage plots"
    )
}

# PDF output
pdf(file = args$output, paper = "special", height = 11.69, width = 8.2677)
plot(graph, newpage = TRUE)
dev.off()