plot_taxa_heatmap: Plot heatmap
In antonioggsousa/micrUBIfuns: Set of functions for microbiome analyses

Description Usage Arguments Value

View source: R/tax.R

Plots an hierarchial heatmap with the package 'ComplexHeatmap' for a given a phyloseq object with 'otu_table', 'tax_table', 'sam_data' (required). If provided a 'tax_rank' the heatmap will be subsetted to the taxonomic rank specified. Samples can be annotated by specifying one or more categorical/factor variables (character) among sample data (in 'sample_variables(physeq)').

plot_taxa_heatmap(
  physeq,
  tax_rank = NULL,
  rm_na = FALSE,
  annot_samples = NULL,
  norm_mth = NULL,
  scale_by = NULL,
  tr_heat = FALSE,
  set_seed = 1024,
  ...
)

`physeq`	phyloseq-class object with 'otu_table', 'tax_table', 'sam_data' slots (required).
`tax_rank`	taxonomic rank (character). One of the taxonomic ranks among the column names of 'tax_table()' of the 'physeq' object given.
`rm_na`	include ('TRUE') or not ('FALSE') NAs (logical), i.e., taxa without classification at the taxonomic level specified at 'tax_rank'. It only works if 'tax_rank' was provided. Otherwise it is ignored.
`annot_samples`	one or more categorical/factor variables (character) among sample data (in 'sample_variables(physeq)'). Default is 'NULL'.
`norm_mth`	normalize/transform the feature table. Default is 'NULL'. One character to pass to 'vegan::decostand()' - one of c("total", "max", "frequency", "normalize", "range", "rank", "standardize", "pa", "chi", "hellinger", "log").
`scale_by`	scale (Z-score) data by "samples" or "taxa" (character). Default is 'NULL'.
`tr_heat`	transpose heatmap. Default is 'FALSE' (logical).
`set_seed`	set seed to allow reproducibility. Default is '1024' (numeric). Set to 'NULL' to turn it off.
`...`	parameters to pass to the function 'ComplexHeatmap::Heatmap()' with the exception of 'matrix'. Also 'top_annotation' (samples in columns) or 'left_annotation' (samples in rows) cannot be specified if 'annot_samples' was specified.