R/color.pal.R

In orionzhou/rmaize: Common bioinformatic utilities

#require(tidyverse)
#require(RColorBrewer)
#require(viridis)
#require(ggsci)

color_palette_plot <- function(fo = '~/projects/rmaize/color.palettes.pdf') {
    tcd = brewer.pal.info
    tc = as_tibble(tcd) %>%
        add_column(pid = rownames(tcd)) %>%
        transmute(set = category, pid = pid, numcol = maxcolors)

    tp = tibble()
    for (i in 1:nrow(tc)) {
        set = tc$set[i]
        numcol = tc$numcol[i]
        pid = tc$pid[i]
        pcols = brewer.pal(numcol, pid)
        tp1 = tibble(set = set, pid = pid, cid = 1:numcol, col = pcols)
        tp = rbind(tp, tp1)
    }
    viridis_pals = c("magma", "inferno", "plasma", "viridis", "cividis")
    for (i in 1:5) {
        set = 'viridis'
        numcol = 12
        pid = viridis_pals[i]
        pcols = viridis_pal(option = pid)(numcol)
        tp1 = tibble(set = set, pid = pid, cid = 1:numcol, col = pcols)
        tp = rbind(tp, tp1)
    }
    sci_pals = c("npg","aaas","nejm","lancet","jama","jco","ucscgb","d3","locuszoom",
                 "igv","uchicago","startrek","tron","futurama","rickandmorty",
                 "simpsons",'gsea','material')
    for (pid in sci_pals) {
        set = 'ggsci'
        palstr = sprintf("pal_%s()(18)", pid)
        pcols = eval(parse(text = palstr))
        pcols = pcols[!is.na(pcols)]
        numcol = length(pcols)
        tp1 = tibble(set = set, pid = pid, cid = 1:numcol, col = pcols)
        tp = rbind(tp, tp1)
    }

    tp = tp %>% mutate(coord = sprintf("%s_%d", pid, cid)) %>%
        mutate(coord = factor(coord, levels = coord))
    p1 = ggplot(tp) +
        geom_tile(aes(x = cid, y = pid, fill = coord), color = 'white', size = 0.5) +
        scale_x_continuous(expand = c(0,0)) +
        scale_y_discrete(expand = c(0,0)) +
        facet_grid(set~., scale = 'free_y', space = 'free_y') + 
        scale_fill_manual(values = tp$col) + 
        theme_bw() +
        theme(legend.position = 'none') +
        theme(axis.ticks.length = unit(0, 'lines')) +
        theme(plot.margin = unit(c(0.3,0.3,0.3,0.3), "lines")) +
        theme(panel.grid.minor = element_blank()) +
        theme(panel.grid.major.y = element_blank()) +
        theme(axis.title.x = element_blank()) +
        theme(axis.title.y = element_blank()) +
        theme(axis.text.x = element_text(size = 8)) +
        theme(axis.text.y = element_text(size = 8, color = "black", angle = 0))
    ggsave(p1, filename = fo, width = 7, height = 9)
}