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annotate coverage_plotting.R @ 15:ffcd42f85b61 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 5eb8570dce4e22fb2759cc16c8e1ce9d304508fe
author artbio
date Sat, 10 Feb 2024 17:15:04 +0000
parents c163574c246f
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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1 #!/usr/bin/env Rscript
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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3 # Help to be printed
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4 hlp_description <- "This script takes a dataframe containing the coverage values for different miRNAs and plots them."
c163574c246f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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5 hlp_usage <- "Usage : coverage_ploting.R --dataframe [FILE] --type ['relative' or 'absolute'] --output [FILE]"
c163574c246f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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6 hlp_dataframe <- "--dataframe\tFILE\tThis is a dataframe containing coverage values obtained from mircounts.py"
c163574c246f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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7 hlp_type <- "--type\t\tSTRING\tType of ploting, either relative or absoute coverage values (default='relative')"
c163574c246f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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8 hlp_output <- "--output\tFILE\tFile to output the pdf to\n"
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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9
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10 hlp <- paste(hlp_description, hlp_usage, hlp_dataframe, hlp_type, hlp_output, sep = "\n")
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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12 # Setup R error handling to go to stderr
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13 options(show.error.messages = FALSE,
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14 error = function() {
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15 cat(geterrmessage(), file = stderr())
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16 q("no", 1, FALSE)
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17 }
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18 )
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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20 library(optparse)
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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21 library(lattice)
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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23 # Get arguments
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24 option_list <- list(
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25 make_option(c("-d", "--dataframe"), type = "character",
c163574c246f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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26 help = "Dataframe containing coverage values obtained from mircounts.py"),
c163574c246f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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27 make_option(c("-t", "--type"), type = "character", default = "relative",
c163574c246f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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28 help = "Type of plotting, either relative or absoute coverage values (default = 'relative')"),
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29 make_option(c("-o", "--output"), type = "character", help = "File to output the pdf to")
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30 )
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31 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
c163574c246f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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32 args <- parse_args(parser)
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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34 if (!("dataframe" %in% names(args)) || !("output" %in% names(args))) {
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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35 stop("'--dataframe' and '--output' parametters are not optional. Please retry.")
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36 }
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38 # Plot
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39 coverage <- read.delim(args$dataframe, header = TRUE)
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40 if (args$type == "relative") {
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41 graph <- xyplot(
ffcd42f85b61 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 5eb8570dce4e22fb2759cc16c8e1ce9d304508fe
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42 Norm_count ~ Norm_offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5,
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43 scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5),
ffcd42f85b61 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 5eb8570dce4e22fb2759cc16c8e1ce9d304508fe
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44 strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15),
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45 as.table = TRUE, xlab = "Normalized Counts", ylab = "Normalized coordinates",
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46 main = "miRNA coverage maps"
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47 )
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48 } else {
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49 graph <- xyplot(
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50 Count ~ Offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5,
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51 scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5),
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52 strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15),
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53 as.table = TRUE, xlab = "Counts", ylab = "Coordinates",
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54 main = "miRNA coverage plots"
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55 )
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56 }
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58 # PDF output
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59 pdf(file = args$output, paper = "special", height = 11.69, width = 8.2677)
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60 plot(graph, newpage = TRUE)
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61 dev.off()