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 viridis inferno

...

Arguments to be passed pheatmap.

Value

A pheatmap plot object.

Examples

library(microbiomeutilities) library(viridis) library(RColorBrewer) data("zackular2014") ps0 <- zackular2014 heat.sample <- plot_taxa_heatmap(ps0, subset.top = 20, VariableA = "DiseaseState", heatcolors =brewer.pal(100, "Blues"), 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.
#> Warning: n too large, allowed maximum for palette Blues is 9 #> Returning the palette you asked for with that many colors