Mercurial > repos > iuc > snpfreqplot

comparison heatmap_for_variants.R @ 2:dc51db22310c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
author iuc
date Fri, 18 Dec 2020 23:48:01 +0000
parents e362b3143cde
children 3d0adeee3f2b
comparison
equal deleted inserted replaced
1:e362b3143cde 2:dc51db22310c
114 ann_final$gene[2:length(ann_final$gene)])) 114 ann_final$gene[2:length(ann_final$gene)]))
115 115
116 # colormanagement 116 # colormanagement
117 my_colors <- colorRampPalette(c("grey93", "brown", "black")) #heatmap 117 my_colors <- colorRampPalette(c("grey93", "brown", "black")) #heatmap
118 count <- length(unique(ann_final$gene)) #annotations (genes) 118 count <- length(unique(ann_final$gene)) #annotations (genes)
119 gene_color <- c(brewer.pal(brewer_color_gene_annotation, n = count)) 119 gene_color <- rep(c(brewer.pal(brewer_color_gene_annotation, n = count)), length.out = count)
120 names(gene_color) <- unique(ann_final$gene) 120 names(gene_color) <- unique(ann_final$gene)
121 121
122 # colormanagement annotations (effect) 122 # colormanagement annotations (effect)
123 ## Define the full set of colors for each effect that we can encounter 123 ## Define the full set of colors for each effect that we can encounter
124 ## This is not bulletproof. The effect names given here were swapped into the 124 ## This is not bulletproof. The effect names given here were swapped into the
159 cols <- unlist(str_split(name, " ")) 159 cols <- unlist(str_split(name, " "))
160 ## first 3 are POS REF ALT, and the rest are optional differences 160 ## first 3 are POS REF ALT, and the rest are optional differences
161 pos_ref_alt <- cols[1:3] 161 pos_ref_alt <- cols[1:3]
162 rest <- "" 162 rest <- ""
163 if (length(cols) > 3) { 163 if (length(cols) > 3) {
164 rest <- paste0(" :: ", paste(cols[4:length(cols)], sep = " ")) 164 rest <- paste0(" :: ", paste0(cols[4:length(cols)], collapse = " "))
165 } 165 }
166 ## Trim the REF or ALT if too long 166 ## Trim the REF or ALT if too long
167 if (str_length(pos_ref_alt[2]) > 3) { 167 if (str_length(pos_ref_alt[2]) > 3) {
168 pos_ref_alt[2] <- paste0(substring(pos_ref_alt[2], 1, 3), "…") 168 pos_ref_alt[2] <- paste0(substring(pos_ref_alt[2], 1, 3), "…")
169 } 169 }
173 ## Join required 173 ## Join required
174 new_name <- paste0(pos_ref_alt[1], " ", 174 new_name <- paste0(pos_ref_alt[1], " ",
175 pos_ref_alt[2], " > ", 175 pos_ref_alt[2], " > ",
176 pos_ref_alt[3]) 176 pos_ref_alt[3])
177 ## Join rest 177 ## Join rest
178 new_name <- paste0(new_name, " ", paste(rest)) 178 new_name <- paste0(new_name, " ", rest)
179 } 179 }
180 180
181 colnames(final) <- sapply(colnames(final), fix_label) 181 colnames(final) <- sapply(colnames(final), fix_label)
182 rownames(ann_final) <- sapply(rownames(ann_final), fix_label) 182 rownames(ann_final) <- sapply(rownames(ann_final), fix_label)
183 ## sanity test 183 ## sanity test