Themes: Standard ggplot2 theme for RIVM Toolbox

In RIVM-IIV-Microbiome/biomeViz: Data visualization for microbiome analytics

Standard ggplot2 theme for RIVM Toolbox

Description

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

Usage

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, ...)

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

Format

An object of class character of length 7.

An object of class list of length 3.

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")

RIVM-IIV-Microbiome/biomeViz documentation built on July 20, 2022, 3:52 a.m.