Mercurial > repos > iuc > ribowaltz_plot

comparison ribowaltz_plot.R @ 1:e25d81465c23 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
author iuc
date Mon, 23 Oct 2023 12:10:37 +0000
parents 8e903cb3f919
children
comparison
equal deleted inserted replaced
0:8e903cb3f919 1:e25d81465c23
116 plot_title = "sample.transcript.length_range" 116 plot_title = "sample.transcript.length_range"
117 ) 117 )
118 print(metaprofile) 118 print(metaprofile)
119 sample_list <- list() 119 sample_list <- list()
120 for (sample_name in names(reads_psite_list)) { 120 for (sample_name in names(reads_psite_list)) {
121 sample_list[[sample_name]] <- c(sample_name) 121 sample_list[[sample_name]] <- c(sample_name)
122 } 122 }
123 metaheatmap <- metaheatmap_psite( 123 metaheatmap <- metaheatmap_psite(
124 reads_psite_list, 124 reads_psite_list,
125 annotation_dt, 125 annotation_dt,
126 sample = sample_list, 126 sample = sample_list,
136 136
137 if (!is.null(opt$params_codon_usage_psite)) { 137 if (!is.null(opt$params_codon_usage_psite)) {
138 pdf("codon_usage.pdf", height = 6, width = 16) 138 pdf("codon_usage.pdf", height = 6, width = 16)
139 json_codon_usage_psite <- fromJSON(opt$params_codon_usage_psite) 139 json_codon_usage_psite <- fromJSON(opt$params_codon_usage_psite)
140 for (sample_name in names(reads_psite_list)) { 140 for (sample_name in names(reads_psite_list)) {
141 cu_barplot <- codon_usage_psite( 141 cu_barplot <- codon_usage_psite(
142 reads_psite_list, 142 reads_psite_list,
143 annotation_dt, 143 annotation_dt,
144 sample = sample_name, 144 sample = sample_name,
145 fastapath = json_codon_usage_psite$fastapath, 145 fastapath = json_codon_usage_psite$fastapath,
146 fasta_genome = FALSE, 146 fasta_genome = FALSE,
147 frequency_normalization = json_codon_usage_psite$frequency 147 frequency_normalization = json_codon_usage_psite$frequency
148 ) 148 )
149 print(cu_barplot[["plot"]]) 149 print(cu_barplot[["plot"]])
150 } 150 }
151 dev.off() 151 dev.off()
152 } 152 }