Standard ggplot2 theme for RIVM Toolbox

Function to extract biomeViz colors as hex codes

List of biomeViz colors

biomeViz palettes

Return function to interpolate a biomeViz color palette

Color scale constructor for biomeViz colors

Fill scale constructor for biomeViz colors

theme_biomViz(base_size = 12, base_family = "")

theme_biomViz_minimal(base_size = 11, base_family = "")

theme_biomViz_bw(base_size = 11, base_family = "")

scale_fill_biomeViz_summer(...)

scale_colour_biomeViz_summer(...)

biomeViz_cols(...)

biomeViz_colors

biomeViz_palettes

biomeViz_pal(palette = "summer", reverse = FALSE, ...)

scale_color_biomeViz(palette = "summer", discrete = TRUE, reverse = FALSE, ...)

scale_fill_biomeViz(palette = "summer", discrete = TRUE, reverse = FALSE, ...)

Format

An object of class character of length 7.

An object of class list of length 3.

Arguments

base_size: Base size
base_family: Base family
...: Additional arguments passed to discrete_scale() or scale_fill_gradientn(), used respectively when discrete is TRUE or FALSE
palette: Character name of palette in biomeViz_palettes
reverse: Boolean indicating whether the palette should be reversed
discrete: Boolean indicating whether color aesthetic is discrete or not

Details

A standard theme for ggplot2 to produce similar aesthetics for RIVM Toolbox.

Examples

library(biomeUtils)
library(biomeViz)
library(microbiome)
library(ggplot2)
library(dplyr)

ps <- FuentesIliGutData %>%
  microbiome::aggregate_taxa("Genus") %>%
  microbiome::transform("compositional")

plotTaxaRaincloud(ps,
                  taxa ="Bacteroides",
                  group_samples_by = "ILI",
                  opacity = 0.25,
                  shape_point = 21) + # combine with ggplot2 for improvements
  labs(y = "Relative abundance",
       x = "",
       subtitle = "Raincloud plot") +
  theme_biomViz_minimal()+
  scale_fill_biomeViz(palette = "viz3") +
  scale_color_biomeViz(palette = "viz3")