Mercurial > repos > artbio > small_rna_signatures

comparison signature.r @ 11:8d3ca9652a5b draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 8691f2575cacd71c971338658198a1324e5f9370"
author artbio
date Sat, 23 Oct 2021 22:55:19 +0000
parents a35e6f9c1d34
children aa5e2c64dff8
comparison
equal deleted inserted replaced
10:68ee7c84d498 11:8d3ca9652a5b
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 = F,
3 #error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) 3 error = function() {
4 cat(geterrmessage(), file = stderr())
5 q("no", 1, F)
6 }
7 )
4 warnings() 8 warnings()
5 9
6 library(RColorBrewer) 10 library(RColorBrewer)
7 library(lattice) 11 library(lattice)
8 library(latticeExtra) 12 library(latticeExtra)
9 library(grid) 13 library(grid)
10 library(gridExtra) 14 library(gridExtra)
11 library(optparse) 15 library(optparse)
12 16
13 option_list <- list( 17 option_list <- list(
14 make_option("--h_dataframe", type="character", help="path to h-signature dataframe"), 18 make_option("--h_dataframe", type = "character",
15 make_option("--z_dataframe", type="character", help="path to z-signature dataframe"), 19 help = "path to h-signature dataframe"),
16 make_option("--plot_method", type = "character", help="How data should be plotted (global or lattice)"), 20 make_option("--z_dataframe", type = "character",
17 make_option("--pdf", type = "character", help="path to the pdf file with plots"), 21 help = "path to z-signature dataframe"),
18 make_option("--title", type = "character", help="Graph Title") 22 make_option("--plot_method", type = "character",
23 help = "How data should be plotted (global or lattice)"),
24 make_option("--pdf", type = "character", help = "path to the pdf file with plots"),
25 make_option("--title", type = "character", help = "Graph Title")
19 ) 26 )
20
21 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) 27 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
22 args = parse_args(parser) 28 args <- parse_args(parser)
23
24
25
26 29
27 # data frames implementation 30 # data frames implementation
28 h_dataframe = read.delim(args$h_dataframe, header=F) 31 h_dataframe <- read.delim(args$h_dataframe, header = F)
29 colnames(h_dataframe) = c("chrom", "overlap", "sig", "z-score") 32 colnames(h_dataframe) <- c("chrom", "overlap", "sig", "z-score")
30 h_dataframe$sig = h_dataframe$sig * 100 # to get probs in % 33 h_dataframe$sig <- h_dataframe$sig * 100 # to get probs in %
31 z_dataframe = read.delim(args$z_dataframe, header=F) 34 z_dataframe <- read.delim(args$z_dataframe, header = F)
32 colnames(z_dataframe) = c("chrom", "overlap", "sig", "z-score") 35 colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score")
33 36
34 # functions 37 # functions
35 globalgraph = function () { 38 globalgraph <- function() {
36 pdf(args$pdf) 39 pdf(args$pdf)
37 par(mfrow=c(2,2),oma = c(0, 0, 3, 0)) 40 par(mfrow = c(2, 2), oma = c(0, 0, 3, 0))
38 41 plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 3)],
39 plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,3)], 42 type = "h", main = "Numbers of pairs", cex.main = 1, xlab = "overlap (nt)",
40 type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)", 43 ylab = "Numbers of pairs", col = "darkslateblue", lwd = 4)
41 ylab="Numbers of pairs", col="darkslateblue", lwd=4)
42 44
43 plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,4)], 45 plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 4)],
44 type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)", 46 type = "l", main = "Number of pairs Z-scores", cex.main = 1, xlab = "overlap (nt)",
45 ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) 47 ylab = "z-score", pch = 19, cex = 0.2, col = "darkslateblue", lwd = 2)
46 48
47 plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,3)], 49 plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 3)],
48 type = "l", main="Overlap probabilities", cex.main=1, xlab="overlap (nt)", 50 type = "l", main = "Overlap probabilities", cex.main = 1,
49 ylab="Probability [%]", ylim=c(0,50), pch=19, col="darkslateblue", lwd=2) 51 xlab = "overlap (nt)",
52 ylab = "Probability [%]", ylim = c(0, 50), pch = 19,
53 col = "darkslateblue", lwd = 2)
50 54
51 plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,4)], 55 plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 4)],
52 type = "l", main="Overlap Probability Z-scores", cex.main=1, 56 type = "l", main = "Overlap Probability Z-scores", cex.main = 1,
53 xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, 57 xlab = "overlap (nt)", ylab = "z-score", pch = 19, cex = 0.2,
54 col="darkslateblue", lwd=2) 58 col = "darkslateblue", lwd = 2)
59 mtext(args$title, outer = TRUE, cex = 1)
60 dev.off()
61 }
55 62
56 mtext(args$title, outer = TRUE, cex=1) 63 treillisgraph <- function(df, ...) {
57 dev.off() 64 pdf(args$pdf, paper = "special", height = 11.69, width = 6)
58 } 65 p <- xyplot(sig ~ overlap | factor(method, levels = unique(method)) + chrom,
59 66 data = df,
60 treillisgraph = function (df, ...) {
61 pdf(args$pdf, paper="special", height=11.69, width=6 ) # 8.2677
62 p = xyplot(sig ~ overlap|factor(method, levels=unique(method))+chrom, data = df,
63 type = "l", 67 type = "l",
64 col='darkblue', 68 col = "darkblue",
65 cex=0.5, 69 cex = 0.5,
66 scales=list(y=list(tick.number=4, relation="free", cex=0.6, rot=0), x=list(cex=0.6, alternating=FALSE)), 70 scales = list(y = list(tick.number = 4, relation = "free", cex = 0.6,
71 rot = 0),
72 x = list(cex = 0.6, alternating = FALSE)),
67 xlab = "Overlap", 73 xlab = "Overlap",
68 ylab = "signature (Nbr of pairs / Overlap prob.)", 74 ylab = "signature (Nbr of pairs / Overlap prob.)",
69 main = args$title, 75 main = args$title,
70 par.strip.text=list(cex=.5), 76 par.strip.text = list(cex = .5),
71 pch=19, lwd =2, 77 pch = 19, lwd = 2,
72 as.table=TRUE, 78 as.table = TRUE,
73 layout=c(2,12), 79 layout = c(2, 12),
74 newpage = T, 80 newpage = T,
75 ...) 81 ...)
76 plot(p) 82 plot(p)
77 dev.off() 83 dev.off()
78 } 84 }
79 85
80 # main 86 # main
81 87
82 if (args$plot_method=="global") { 88 if (args$plot_method == "global") {
83 globalgraph() 89 globalgraph()
84 } 90 }
85 91
86 if(args$plot_method=="lattice") { 92 if (args$plot_method == "lattice") {
87 # rearrange dataframes 93 # rearrange dataframes
88 h_sig = h_dataframe[,c(1,2,3)] 94 h_sig <- h_dataframe[, c(1, 2, 3)]
89 h_sig = cbind(rep("Overlap Prob (%)", length(h_sig[,1])), h_sig) 95 h_sig <- cbind(rep("Overlap Prob (%)", length(h_sig[, 1])), h_sig)
90 colnames(h_sig) = c("method", "chrom", "overlap", "sig") 96 colnames(h_sig) <- c("method", "chrom", "overlap", "sig")
91 z_pairs = z_dataframe[,c(1,2,3)] 97 z_pairs <- z_dataframe[, c(1, 2, 3)]
92 z_pairs = cbind(rep("Nbr of pairs", length(z_pairs[,1])), z_pairs) 98 z_pairs <- cbind(rep("Nbr of pairs", length(z_pairs[, 1])), z_pairs)
93 colnames(z_pairs) = c("method", "chrom", "overlap", "sig") 99 colnames(z_pairs) <- c("method", "chrom", "overlap", "sig")
94 lattice_df = rbind(z_pairs, h_sig) 100 lattice_df <- rbind(z_pairs, h_sig)
95 par.settings.treillis=list(strip.background = list( 101 par_settings_treillis <- list(strip.background = list(
96 col = c("lightblue", "lightgreen"))) 102 col = c("lightblue", "lightgreen")))
97 103 treillisgraph(lattice_df, par.settings = par_settings_treillis)
98 treillisgraph(lattice_df, par.settings=par.settings.treillis)
99 } 104 }