phyloseq-class
and pheatmap
plot_taxa_heatmap.Rd
Plot heatmap using phyloseq-class
object as input.
plot_taxa_heatmap(x, subset.top, transformation, VariableA, heatcolors = NULL, ...)
x |
|
---|---|
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 |
... | Arguments to be passed |
A pheatmap
plot object.
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")#>#>#>#>#> 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