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comparison 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
children
comparison
equal deleted inserted replaced
14:c163574c246f 15:ffcd42f85b61
8 hlp_output <- "--output\tFILE\tFile to output the pdf to\n" 8 hlp_output <- "--output\tFILE\tFile to output the pdf to\n"
9 9
10 hlp <- paste(hlp_description, hlp_usage, hlp_dataframe, hlp_type, hlp_output, sep = "\n") 10 hlp <- paste(hlp_description, hlp_usage, hlp_dataframe, hlp_type, hlp_output, sep = "\n")
11 11
12 # Setup R error handling to go to stderr 12 # Setup R error handling to go to stderr
13 options(show.error.messages = F, 13 options(show.error.messages = FALSE,
14 error = function() { 14 error = function() {
15 cat(geterrmessage(), file = stderr()); q("no", 1, F) 15 cat(geterrmessage(), file = stderr())
16 q("no", 1, FALSE)
16 } 17 }
17 ) 18 )
18 19
19 library(optparse) 20 library(optparse)
20 library(lattice) 21 library(lattice)
24 make_option(c("-d", "--dataframe"), type = "character", 25 make_option(c("-d", "--dataframe"), type = "character",
25 help = "Dataframe containing coverage values obtained from mircounts.py"), 26 help = "Dataframe containing coverage values obtained from mircounts.py"),
26 make_option(c("-t", "--type"), type = "character", default = "relative", 27 make_option(c("-t", "--type"), type = "character", default = "relative",
27 help = "Type of plotting, either relative or absoute coverage values (default = 'relative')"), 28 help = "Type of plotting, either relative or absoute coverage values (default = 'relative')"),
28 make_option(c("-o", "--output"), type = "character", help = "File to output the pdf to") 29 make_option(c("-o", "--output"), type = "character", help = "File to output the pdf to")
29 ) 30 )
30 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) 31 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
31 args <- parse_args(parser) 32 args <- parse_args(parser)
32 33
33 if (!("dataframe" %in% names(args)) || !("output" %in% names(args))) { 34 if (!("dataframe" %in% names(args)) || !("output" %in% names(args))) {
34 stop("'--dataframe' and '--output' parametters are not optional. Please retry.") 35 stop("'--dataframe' and '--output' parametters are not optional. Please retry.")
35 } 36 }
36 37
37 # Plot 38 # Plot
38 coverage <- read.delim(args$dataframe, header = T) 39 coverage <- read.delim(args$dataframe, header = TRUE)
39 if (args$type == "relative") { 40 if (args$type == "relative") {
40 graph <- xyplot(Norm_count ~ Norm_offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5, 41 graph <- xyplot(
41 scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5), 42 Norm_count ~ Norm_offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5,
42 strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15), 43 scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5),
43 as.table = T, xlab = "Normalized Counts", ylab = "Normalized coordinates", 44 strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15),
44 main = "miRNA coverage maps") 45 as.table = TRUE, xlab = "Normalized Counts", ylab = "Normalized coordinates",
46 main = "miRNA coverage maps"
47 )
45 } else { 48 } else {
46 graph <- xyplot(Count ~ Offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5, 49 graph <- xyplot(
47 scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5), 50 Count ~ Offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5,
48 strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15), 51 scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5),
49 as.table = T, xlab = "Counts", ylab = "Coordinates", 52 strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15),
50 main = "miRNA coverage plots") 53 as.table = TRUE, xlab = "Counts", ylab = "Coordinates",
54 main = "miRNA coverage plots"
55 )
51 } 56 }
52 57
53 # PDF output 58 # PDF output
54 pdf(file = args$output, paper = "special", height = 11.69, width = 8.2677) 59 pdf(file = args$output, paper = "special", height = 11.69, width = 8.2677)
55 plot(graph, newpage = T) 60 plot(graph, newpage = TRUE)
56 dev.off() 61 dev.off()