Heatmap using phyloseq-class and pheatmap

Source: R/plot_taxa_heatmap.R

Plot heatmap using phyloseq-class object as input.

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

Sudarshan A. Shetty (sudarshanshetty9@gmail.com)

Examples


library(microbiomeutilities)
library(viridis)
#> Loading required package: viridisLite
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"
)
#> Top 20 OTUs selected 
#> log10, if zeros in data then log10(1+x) will be used
#> First top taxa were selected and 
#> then abundances tranformed to log10(1+X)
#> Warning: OTU table contains zeroes. Using log10(1 + x) transform.