A list of palettes for use in data visualization
Examples
# \dontrun{
if (interactive()) {
library(stringr)
library(RColorBrewer)
library(Redmonder)
library(rcartocolor)
library(nord)
library(viridis)
library(pals)
library(dichromat)
library(jcolors)
library(scales)
syspals <- utils::getFromNamespace("syspals", "pals")
brewer.pal.info <- RColorBrewer::brewer.pal.info
ggsci_db <- utils::getFromNamespace("ggsci_db", "ggsci")
redmonder.pal.info <- Redmonder::redmonder.pal.info
metacartocolors <- rcartocolor::metacartocolors
rownames(metacartocolors) <- metacartocolors$Name
nord_palettes <- nord::nord_palettes
viridis_names <- c("magma", "inferno", "plasma", "viridis", "cividis", "rocket",
"mako", "turbo")
viridis_palettes <- lapply(setNames(viridis_names, viridis_names),
function(x) viridis::viridis(100, option = x))
ocean_names <- names(syspals)[grep("ocean", names(syspals))]
ocean_palettes <- syspals[ocean_names]
dichromat_palettes <- dichromat::colorschemes
jcolors_names <- paste0("jcolors-", c("default", "pal2", "pal3", "pal4", "pal5",
"pal6", "pal7", "pal8", "pal9", "pal10", "pal11", "pal12", "rainbow"))
custom_names <- c("jet", "simspec", "GdRd")
custom_palettes <- list(
oompaBase::jetColors(N = 100),
c("#c22b86", "#f769a1", "#fcc5c1", "#253777", "#1d92c0", "#9ec9e1", "#015b33",
"#42aa5e", "#d9f0a2", "#E66F00", "#f18c28", "#FFBB61"),
c("gold", "red3")
)
names(custom_palettes) <- custom_names
seurat_discrete_palettes <- list(
alphabet = c(
"#F0A0FF", "#0075DC", "#993F00", "#4C005C", "#191919", "#005C31",
"#2BCE48", "#FFCC99", "#808080", "#94FFB5", "#8F7C00", "#9DCC00",
"#C20088", "#003380", "#FFA405", "#FFA8BB", "#426600", "#FF0010",
"#5EF1F2", "#00998F", "#E0FF66", "#740AFF", "#990000", "#FFFF80",
"#FFE100", "#FF5005"
),
alphabet2 = c(
"#AA0DFE", "#3283FE", "#85660D", "#782AB6", "#565656", "#1C8356",
"#16FF32", "#F7E1A0", "#E2E2E2", "#1CBE4F", "#C4451C", "#DEA0FD",
"#FE00FA", "#325A9B", "#FEAF16", "#F8A19F", "#90AD1C", "#F6222E",
"#1CFFCE", "#2ED9FF", "#B10DA1", "#C075A6", "#FC1CBF", "#B00068",
"#FBE426", "#FA0087"
),
glasbey = c(
"#0000FF", "#FF0000", "#00FF00", "#000033", "#FF00B6", "#005300",
"#FFD300", "#009FFF", "#9A4D42", "#00FFBE", "#783FC1", "#1F9698",
"#FFACFD", "#B1CC71", "#F1085C", "#FE8F42", "#DD00FF", "#201A01",
"#720055", "#766C95", "#02AD24", "#C8FF00", "#886C00", "#FFB79F",
"#858567", "#A10300", "#14F9FF", "#00479E", "#DC5E93", "#93D4FF",
"#004CFF", "#F2F318"
),
polychrome = c(
"#5A5156", "#E4E1E3", "#F6222E", "#FE00FA", "#16FF32", "#3283FE",
"#FEAF16", "#B00068", "#1CFFCE", "#90AD1C", "#2ED9FF", "#DEA0FD",
"#AA0DFE", "#F8A19F", "#325A9B", "#C4451C", "#1C8356", "#85660D",
"#B10DA1", "#FBE426", "#1CBE4F", "#FA0087", "#FC1CBF", "#F7E1A0",
"#C075A6", "#782AB6", "#AAF400", "#BDCDFF", "#822E1C", "#B5EFB5",
"#7ED7D1", "#1C7F93", "#D85FF7", "#683B79", "#66B0FF", "#3B00FB"
),
stepped = c(
"#990F26", "#B33E52", "#CC7A88", "#E6B8BF", "#99600F", "#B3823E",
"#CCAA7A", "#E6D2B8", "#54990F", "#78B33E", "#A3CC7A", "#CFE6B8",
"#0F8299", "#3E9FB3", "#7ABECC", "#B8DEE6", "#3D0F99", "#653EB3",
"#967ACC", "#C7B8E6", "#333333", "#666666", "#999999", "#CCCCCC"
),
parade = c(
'#ff6969', '#9b37ff', '#cd3737', '#69cdff', '#ffff69', '#69cdcd',
'#9b379b', '#3737cd', '#ffff9b', '#cdff69', '#ff9b37', '#37ffff',
'#9b69ff', '#37cd69', '#ff3769', '#ff3737', '#37ff9b', '#cdcd37',
'#3769cd', '#37cdff', '#9b3737', '#ff699b', '#9b9bff', '#cd9b37',
'#69ff37', '#cd3769', '#cd69cd', '#cd6937', '#3737ff', '#cdcd69',
'#ff9b69', '#cd37cd', '#9bff37', '#cd379b', '#cd6969', '#69ff9b',
'#ff379b', '#9bff9b', '#6937ff', '#69cd37', '#cdff37', '#9bff69',
'#9b37cd', '#ff37ff', '#ff37cd', '#ffff37', '#37cd9b', '#379bff',
'#ffcd37', '#379b37', '#ff9bff', '#379b9b', '#69ffcd', '#379bcd',
'#ff69ff', '#ff9b9b', '#37ff69', '#ff6937', '#6969ff', '#699bff',
'#ffcd69', '#69ffff', '#37ff37', '#6937cd', '#37cd37', '#3769ff',
'#cd69ff', '#6969cd', '#9bcd37', '#69ff69', '#37cdcd', '#cd37ff',
'#37379b', '#37ffcd', '#69cd69'
)
)
seurat_continuous_palettes <- list(
seurat.16 = hue_pal()(16),
seurat.32 = hue_pal()(32),
seurat.64 = hue_pal()(64)
)
palette_list <- list()
all_colors <- c(
rownames(brewer.pal.info), names(ggsci_db), rownames(redmonder.pal.info),
rownames(metacartocolors), names(nord_palettes), names(viridis_palettes),
ocean_names, names(dichromat_palettes), jcolors_names, names(seurat_palettes),
names(seurat_continuous_palettes), custom_names
)
for (pal in all_colors) {
if (!pal %in% all_colors) {
stop(paste0("Invalid pal Must be one of ", paste0(all_colors, collapse = ",")))
}
if (pal %in% rownames(brewer.pal.info)) {
pal_n <- brewer.pal.info[pal, "maxcolors"]
pal_category <- brewer.pal.info[pal, "category"]
if (pal_category == "div") {
palcolor <- rev(brewer.pal(name = pal, n = pal_n))
} else {
if (pal == "Paired") {
palcolor <- brewer.pal(12, "Paired")[c(1:4, 7, 8, 5, 6, 9, 10, 11, 12)]
} else {
palcolor <- brewer.pal(name = pal, n = pal_n)
}
}
if (pal_category == "qual") {
attr(palcolor, "type") <- "discrete"
} else {
attr(palcolor, "type") <- "continuous"
}
} else if (pal %in% names(ggsci_db)) {
if (pal %in% c("d3", "uchicago", "material")) {
for (subpal in names(ggsci_db[[pal]])) {
palcolor <- ggsci_db[[pal]][[subpal]]
if (pal == "material") {
attr(palcolor, "type") <- "continuous"
} else {
attr(palcolor, "type") <- "discrete"
}
palette_list[[paste0(pal, "-", subpal)]] <- palcolor
}
next
} else {
palcolor <- ggsci_db[[pal]][[1]]
if (pal == "gsea") {
attr(palcolor, "type") <- "continuous"
} else {
attr(palcolor, "type") <- "discrete"
}
}
} else if (pal %in% rownames(redmonder.pal.info)) {
pal_n <- redmonder.pal.info[pal, "maxcolors"]
pal_category <- redmonder.pal.info[pal, "category"]
if (pal_category == "div") {
palcolor <- rev(redmonder.pal(name = pal, n = pal_n))
} else {
palcolor <- redmonder.pal(name = pal, n = pal_n)
}
if (pal_category == "qual") {
attr(palcolor, "type") <- "discrete"
} else {
attr(palcolor, "type") <- "continuous"
}
} else if (pal %in% rownames(metacartocolors)) {
pal_n <- metacartocolors[pal, "Max_n"]
palcolor <- carto_pal(name = pal, n = pal_n)
if (pal_category == "qualitative") {
attr(palcolor, "type") <- "discrete"
} else {
attr(palcolor, "type") <- "continuous"
}
} else if (pal %in% names(nord_palettes)) {
palcolor <- nord_palettes[[pal]]
attr(palcolor, "type") <- "discrete"
} else if (pal %in% names(viridis_palettes)) {
palcolor <- viridis_palettes[[pal]]
attr(palcolor, "type") <- "continuous"
} else if (pal %in% names(ocean_palettes)) {
palcolor <- ocean_palettes[[pal]]
attr(palcolor, "type") <- "continuous"
} else if (pal %in% names(dichromat_palettes)) {
palcolor <- dichromat_palettes[[pal]]
if (pal %in% c("Categorical.12", "SteppedSequential.5")) {
attr(palcolor, "type") <- "discrete"
} else {
attr(palcolor, "type") <- "continuous"
}
} else if (pal %in% jcolors_names) {
palcolor <- jcolors(palette = gsub("jcolors-", "", pal))
if (pal %in% paste0("jcolors-", c("pal10", "pal11", "pal12", "rainbow"))) {
attr(palcolor, "type") <- "continuous"
} else {
attr(palcolor, "type") <- "discrete"
}
} else if (pal %in% custom_names) {
palcolor <- custom_palettes[[pal]]
if (pal %in% c("jet")) {
attr(palcolor, "type") <- "continuous"
} else {
attr(palcolor, "type") <- "discrete"
}
} else if (pal %in% names(seurat_discrete_palettes)) {
palcolor <- seurat_discrete_palettes[[pal]]
attr(palcolor, "type") <- "discrete"
} else if (pal %in% names(seurat_continuous_palettes)) {
palcolor <- seurat_continuous_palettes[[pal]]
attr(palcolor, "type") <- "continuous"
}
palette_list[[pal]] <- palcolor
}
}
# }