plot_taxa_heatmap: Heatmap using 'phyloseq-class' and 'pheatmap'

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Heatmap using phyloseq-class and pheatmap

Description

Plot heatmap using phyloseq-class object as input.

Usage

plot_taxa_heatmap(
  x,
  subset.top,
  transformation,
  VariableA,
  heatcolors = NULL,
  ...
)

Arguments

x	phyloseq-class object.
subset.top	either NA or number of Top OTUs to use for plotting.
transformation	either 'log10', 'clr','Z', 'compositional', or NA
VariableA	main variable of Interest.
heatcolors	is the option for colors in pheatmap. Default is to use Spectral
...	Arguments to be passed pheatmap.

Value

A pheatmap plot object.

Author(s)

Sudarshan A. Shetty ([e-mail])

Examples

library(microbiomeutilities)
library(viridis)
library(RColorBrewer)
data("zackular2014")
ps0 <- zackular2014

heat.sample <- plot_taxa_heatmap(ps0,
  subset.top = 20,
  VariableA = "DiseaseState",
  heatcolors = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100),
  transformation = "log10"
)

microsud/microbiomeutilities documentation built on Nov. 29, 2022, 12:18 a.m.