ps_pheatmap: Make pheatmap directly from a phyloseq object

In Russel88/MicEco: Various functions for microbial community data

Make pheatmap directly from a phyloseq object

Description

Make pheatmap directly from a phyloseq object, including agglomoration and filtering. Default color map is viridis with absent taxa as black.

Usage

ps_pheatmap(
  ps,
  annot_samp = NULL,
  annot_taxa = NULL,
  relative = TRUE,
  log10 = TRUE,
  tax_agg = NULL,
  order_taxa = TRUE,
  min_samples = 1,
  min_reads = 1,
  min_abundance = 0,
  label_rank = NULL,
  color = c("black", viridis::viridis(10)),
  ...
)

Arguments

ps	A phyloseq object
annot_samp	Sample variables to annotate with
annot_taxa	Taxa variables to annotate with
relative	If TRUE, abundances total sum scaled. Default TRUE
log10	If TRUE, log10 transform abundances. Default TRUE
tax_agg	Taxa rank to agglomorate. Default NULL
order_taxa	If TRUE, taxa are ordered from most to least abundant. Default TRUE
min_samples	Minimum number of samples the features should be present in. Default 1
min_reads	Minimum number of total reads the features should have. Default 1
min_abundance	Minimum mean relative abundance features should have. Default 0
label_rank	Taxa rank to label the taxa. If NULL will label by taxa_names(ps). Default NULL
color	Color palette. Default viridis with absent
...	Additional arguments to pheatmap function

Value

A pheatmap

Russel88/MicEco documentation built on Nov. 24, 2022, 2:33 a.m.