Mercurial > repos > iuc > ribowaltz_plot

comparison ribowaltz_plot.R @ 0:4fbc0799c63d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
author iuc
date Thu, 22 Sep 2022 20:28:25 +0000
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-1:000000000000 0:4fbc0799c63d
1 # setup R error handling to go to stderr
2 options(show.error.messages = FALSE, error = function() {
3 cat(geterrmessage(), file = stderr())
4 q("no", 1, FALSE)
5 })
6
7 # we need that to not crash galaxy with an UTF8 error on German LC settings.
8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
9 library("getopt")
10 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
11 args <- commandArgs(trailingOnly = TRUE)
12
13 # get options, using the spec as defined by the enclosed list.
14 # we read the options from the default: commandArgs(TRUE).
15 spec <- matrix(c(
16 "quiet", "q", 0, "logical",
17 "help", "h", 0, "logical",
18 "input_rdata", "i", 1, "character",
19 "params_rlength_distr", "r", 0, "character",
20 "params_rends_heat", "e", 0, "character",
21 "region_psite_plot", "R", 0, "logical",
22 "params_trint_periodicity", "t", 0, "character",
23 "params_metaplots", "m", 0, "character",
24 "params_codon_usage_psite", "u", 0, "character"
25 ), byrow = TRUE, ncol = 4)
26 opt <- getopt(spec)
27
28 # if help was asked for print a friendly message
29 # and exit with a non-zero error code
30 if (!is.null(opt$help)) {
31 cat(getopt(spec, usage = TRUE))
32 q(status = 1)
33 }
34
35 verbose <- is.null(opt$quiet)
36
37 library("riboWaltz")
38 library("jsonlite")
39
40 load(opt$input_rdata)
41
42 if (!is.null(opt$params_rlength_distr)) {
43 pdf("read_lengths.pdf")
44 json_rlength_distr <- fromJSON(opt$params_rlength_distr)
45 length_dist <- rlength_distr(
46 reads_psite_list,
47 sample = names(reads_psite_list),
48 cl = json_rlength_distr$cl,
49 multisamples = json_rlength_distr$multisamples,
50 plot_style = json_rlength_distr$plot_style
51 )
52 print(length_dist)
53 dev.off()
54 }
55
56 if (!is.null(opt$params_rends_heat)) {
57 pdf("read_ends_heatmap.pdf", height = 5 * length(reads_psite_list), width = 15)
58 json_rends_heat <- fromJSON(opt$params_rends_heat)
59 for (sample_name in names(reads_psite_list)) {
60 ends_heatmap <- rends_heat(
61 reads_psite_list,
62 annotation_dt,
63 sample = sample_name,
64 cl = json_rends_heat$cl,
65 utr5l = json_rends_heat$utr5l,
66 cdsl = json_rends_heat$cdsl,
67 utr3l = json_rends_heat$utr3l
68 )
69 print(ends_heatmap[["plot"]])
70 }
71 dev.off()
72 }
73
74 if (!is.null(opt$region_psite_plot)) {
75 pdf("psites_per_region.pdf", height = 12, width = 7 * length(reads_psite_list))
76 psite_region <- region_psite(reads_psite_list, annotation_dt, sample = names(reads_psite_list))
77 print(psite_region[["plot"]])
78 dev.off()
79 }
80
81 if (!is.null(opt$params_trint_periodicity)) {
82 pdf("trinucleotide_periodicity.pdf", height = 6 * length(reads_psite_list), width = 10)
83 json_trint_periodicity <- fromJSON(opt$params_trint_periodicity)
84 frames_stratified <- frame_psite_length(
85 reads_psite_list,
86 sample = names(reads_psite_list),
87 cl = json_trint_periodicity$cl,
88 region = json_trint_periodicity$region,
89 length_range = json_trint_periodicity$length_range
90 )
91 frames_stratified[["plot"]]
92 frames <- frame_psite_length(
93 reads_psite_list,
94 sample = names(reads_psite_list),
95 region = json_trint_periodicity$region,
96 length_range = json_trint_periodicity$length_range
97 )
98 print(frames[["plot"]])
99 dev.off()
100 }
101
102 if (!is.null(opt$params_metaplots)) {
103 pdf("metaplots.pdf", height = 5 * length(reads_psite_list), width = 24)
104 json_metaplots <- fromJSON(opt$params_metaplots)
105 metaprofile <- metaprofile_psite(
106 reads_psite_list,
107 annotation_dt,
108 sample = names(reads_psite_list),
109 multisamples = json_metaplots$multisamples,
110 plot_style = json_metaplots$plot_style,
111 length_range = json_metaplots$length_range,
112 frequency = json_metaplots$frequency,
113 utr5l = json_metaplots$utr5l,
114 cdsl = json_metaplots$cdsl,
115 utr3l = json_metaplots$utr3l,
116 plot_title = "sample.transcript.length_range"
117 )
118 print(metaprofile)
119 sample_list <- list()
120 for (sample_name in names(reads_psite_list)) {
121 sample_list[[sample_name]] <- c(sample_name)
122 }
123 metaheatmap <- metaheatmap_psite(
124 reads_psite_list,
125 annotation_dt,
126 sample = sample_list,
127 length_range = json_metaplots$length_range,
128 utr5l = json_metaplots$utr5l,
129 cdsl = json_metaplots$cdsl,
130 utr3l = json_metaplots$utr3l,
131 plot_title = "Comparison metaheatmap"
132 )
133 print(metaheatmap[["plot"]])
134 dev.off()
135 }
136
137 if (!is.null(opt$params_codon_usage_psite)) {
138 pdf("codon_usage.pdf", height = 6, width = 16)
139 json_codon_usage_psite <- fromJSON(opt$params_codon_usage_psite)
140 for (sample_name in names(reads_psite_list)) {
141 cu_barplot <- codon_usage_psite(
142 reads_psite_list,
143 annotation_dt,
144 sample = sample_name,
145 fastapath = json_codon_usage_psite$fastapath,
146 fasta_genome = FALSE,
147 frequency_normalization = json_codon_usage_psite$frequency
148 )
149 print(cu_barplot[["plot"]])
150 }
151 dev.off()
152 }