plot_taxa_heatmap: Heatmap using phyloseq and pheatmap

In microsud/microbiomeutilities-shiny: microbiomeutilities: An R package with utility functions for the microbiome R package

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 viridis inferno
...	Arguments to be passed pheatmap.

Value

A pheatmap plot object.

Author(s)

Sudarshan A. Shetty ([e-mail])

Examples

## Not run: 
  # Example data
    library(microbiomeutilities)
    library(viridis)
    data("biogeogut")
    ps0 <- biogeogut

    p <- plot_taxa_heatmap(ps, taxonomic.level = "Genus", subset.top = 10,
    VariableA = "SampleType",
    heatcolors = NA)
          
## End(Not run)

microsud/microbiomeutilities-shiny documentation built on May 7, 2019, 9:38 a.m.