plotTidyHeatmap: Creates a Heatmap using 'TidyHeatmap' and 'ComplexHeatmap'

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

Creates a Heatmap using 'TidyHeatmap' and 'ComplexHeatmap'

Description

Creates a Heatmap using 'TidyHeatmap' and 'ComplexHeatmap'

Usage

plotTidyHeatmap(
  x,
  select_taxa = NULL,
  group_samples_by = NULL,
  add_taxa_label = TRUE,
  ...
)

Arguments

x	phyloseq-class object.
select_taxa	Features to plot.
group_samples_by	A column in sample_data to group tiles.
add_taxa_label	Logical. Default is TRUE.
...	Arguments forwarded to tidyHeatmap::heatmap and ComplexHeatmap::Heatmap.

Details

A TidyHeatmap plotting wrapper for phyloseq-class object.

Value

a heatmap object.

Author(s)

Sudarshan A. Shetty

References

Shetty SA (2021). Data visualization for microbiome analytics. https://github.com/microsud/biomeViz

Examples

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

ps <- FuentesIliGutData %>%
         microbiome::transform("compositional")
select_taxa <- findTopTaxa(ps, top= 10, method="mean")

plotTidyHeatmap(ps, select_taxa = select_taxa,
                group_samples_by = "ILI",
                add_taxa_label = FALSE,
                cluster_rows = FALSE,
                .scale = "none",
                transform = NULL,
                palette_value = c("red", "white", "blue"))

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