comparison heatmap_for_variants.R @ 2:dc51db22310c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"

1:e362b3143cde

                      ann_final$gene[2:length(ann_final$gene)]))

                                        # colormanagement
my_colors <- colorRampPalette(c("grey93", "brown", "black")) #heatmap
count <- length(unique(ann_final$gene))                     #annotations (genes)
gene_color <- c(brewer.pal(brewer_color_gene_annotation, n = count))
names(gene_color) <- unique(ann_final$gene)

                                        # colormanagement annotations (effect)
## Define the full set of colors for each effect that we can encounter
## This is not bulletproof. The effect names given here were swapped into the

    cols <- unlist(str_split(name, " "))
    ## first 3 are POS REF ALT, and the rest are optional differences
    pos_ref_alt <- cols[1:3]
    rest <- ""
    if (length(cols) > 3) {
        rest <- paste0(" :: ", paste(cols[4:length(cols)], sep = " "))
    }
    ## Trim the REF or ALT if too long
    if (str_length(pos_ref_alt[2]) > 3) {
        pos_ref_alt[2] <- paste0(substring(pos_ref_alt[2], 1, 3), "…")
    }

    ## Join required
    new_name <- paste0(pos_ref_alt[1], " ",
                       pos_ref_alt[2], " > ",
                       pos_ref_alt[3])
    ## Join rest
    new_name <- paste0(new_name, " ", paste(rest))
}

colnames(final) <- sapply(colnames(final), fix_label)
rownames(ann_final) <- sapply(rownames(ann_final), fix_label)
## sanity test

2:dc51db22310c

                      ann_final$gene[2:length(ann_final$gene)]))

                                        # colormanagement
my_colors <- colorRampPalette(c("grey93", "brown", "black")) #heatmap
count <- length(unique(ann_final$gene))                     #annotations (genes)
gene_color <- rep(c(brewer.pal(brewer_color_gene_annotation, n = count)), length.out = count)
names(gene_color) <- unique(ann_final$gene)

                                        # colormanagement annotations (effect)
## Define the full set of colors for each effect that we can encounter
## This is not bulletproof. The effect names given here were swapped into the

    cols <- unlist(str_split(name, " "))
    ## first 3 are POS REF ALT, and the rest are optional differences
    pos_ref_alt <- cols[1:3]
    rest <- ""
    if (length(cols) > 3) {
        rest <- paste0(" :: ", paste0(cols[4:length(cols)], collapse = " "))
    }
    ## Trim the REF or ALT if too long
    if (str_length(pos_ref_alt[2]) > 3) {
        pos_ref_alt[2] <- paste0(substring(pos_ref_alt[2], 1, 3), "…")
    }

    ## Join required
    new_name <- paste0(pos_ref_alt[1], " ",
                       pos_ref_alt[2], " > ",
                       pos_ref_alt[3])
    ## Join rest
    new_name <- paste0(new_name, " ", rest)
}

colnames(final) <- sapply(colnames(final), fix_label)
rownames(ann_final) <- sapply(rownames(ann_final), fix_label)
## sanity test