Make a fixed taxa colour palette e.g. for comp_barplot

Source: R/tax_palette.R

Makes a named palette vector from your phyloseq dataset considering overall abundance to assign colours (or some other sorting)

tax_palette(
  data,
  rank,
  n,
  by = sum,
  pal = "brewerPlus",
  add = c(other = "lightgrey"),
  ...
)

Arguments

data

phyloseq or psExtra

rank

taxonomic rank name or "unique"

n

number of colours / taxa (not including "other")

by

tax sorting method for tax_sort e.g. sum

pal

palette name from distinct_palette function

add

name = value pairs appended to end of output, or NA for none

...

other args are passed to tax_sort

Value

named character vector

Examples

library(ggplot2)
data(dietswap, package = "microbiome")

myPal <- tax_palette(dietswap, rank = "Genus", pal = "brewerPlus", n = 40)
myPal %>% tax_palette_plot() # just to check the palette


# plot one subset of data
dietswap %>%
  ps_filter(nationality == "AFR", timepoint == 1, sex == "male") %>%
  comp_barplot(
    tax_level = "Genus", n_taxa = 15,
    bar_outline_colour = NA, bar_width = 0.7,
    palette = myPal, label = NULL
  )


# plot a different subset of data (top taxa differ but colours are the same)
dietswap %>%
  ps_filter(nationality != "AFR", timepoint == 1, sex == "male") %>%
  comp_barplot(
    tax_level = "Genus", n_taxa = 15,
    bar_outline_colour = NA, bar_width = 0.7,
    palette = myPal, label = NULL
  )