PlotHeatmap: Plot a standard rainbow heatmap with faceting.

In eclarke/eclectic: Miscellaneous functions for bioinformatics data

Description

Uses the output of MakeHeatmapData to display a heatmap with (by default) SampleIDs on the x-axis and a minimum taxonomic rank of Genus on the y-axis.

Usage

PlotHeatmap(heatmap.data, use.reads = TRUE, threshold = 0.6,
  x.text = TRUE, x.axis = "SampleID")

Arguments

heatmap.data	the dataframe from MakeHeatmapData
use.reads	if TRUE, plot the raw readcounts; if FALSE, use proportions. Raw readcounts are subject to biases from uneven library size but can be preferable for low-biomass or extremely sparse samples, as proportions can be distorting.
threshold	at what relative proportion the color scale goes to red. This should be adjusted such that there is only one red cell per row.
x.text	display labels on the x-axis?
x.axis	name of factor to be used to define the x-axis (must exist in heatmap.data)

eclarke/eclectic documentation built on May 15, 2019, 7:54 p.m.