Mercurial > repos > artbio > small_rna_signatures

comparison signature.r @ 12:aa5e2c64dff8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a
author artbio
date Sat, 22 Oct 2022 23:49:52 +0000
parents 8d3ca9652a5b
children 5150d641d515
comparison
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11:8d3ca9652a5b 12:aa5e2c64dff8
1 ## Setup R error handling to go to stderr 1 ## Setup R error handling to go to stderr
2 options(show.error.messages = F, 2 options(show.error.messages = FALSE,
3 error = function() { 3 error = function() {
4 cat(geterrmessage(), file = stderr()) 4 cat(geterrmessage(), file = stderr())
5 q("no", 1, F) 5 q("no", 1, FALSE)
6 } 6 }
7 ) 7 )
8 warnings() 8 warnings()
9 9
10 library(RColorBrewer) 10 library(RColorBrewer)
24 make_option("--pdf", type = "character", help = "path to the pdf file with plots"), 24 make_option("--pdf", type = "character", help = "path to the pdf file with plots"),
25 make_option("--title", type = "character", help = "Graph Title") 25 make_option("--title", type = "character", help = "Graph Title")
26 ) 26 )
27 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) 27 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
28 args <- parse_args(parser) 28 args <- parse_args(parser)
29 29
30 # data frames implementation 30 # data frames implementation
31 h_dataframe <- read.delim(args$h_dataframe, header = F) 31 h_dataframe <- read.delim(args$h_dataframe, header = FALSE)
32 colnames(h_dataframe) <- c("chrom", "overlap", "sig", "z-score") 32 colnames(h_dataframe) <- c("chrom", "overlap", "sig", "z-score")
33 h_dataframe$sig <- h_dataframe$sig * 100 # to get probs in % 33 h_dataframe$sig <- h_dataframe$sig * 100 # to get probs in %
34 z_dataframe <- read.delim(args$z_dataframe, header = F) 34 z_dataframe <- read.delim(args$z_dataframe, header = FALSE)
35 colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score") 35 colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score")
36 36
37 # functions 37 # functions
38 globalgraph <- function() { 38 globalgraph <- function() {
39 pdf(args$pdf) 39 pdf(args$pdf)
75 main = args$title, 75 main = args$title,
76 par.strip.text = list(cex = .5), 76 par.strip.text = list(cex = .5),
77 pch = 19, lwd = 2, 77 pch = 19, lwd = 2,
78 as.table = TRUE, 78 as.table = TRUE,
79 layout = c(2, 12), 79 layout = c(2, 12),
80 newpage = T, 80 newpage = TRUE,
81 ...) 81 ...)
82 plot(p) 82 plot(p)
83 dev.off() 83 dev.off()
84 } 84 }
85 85