plotHeatmap: Plot heatmap

In zoecastillo/microbiomeExplorer: Microbiome Exploration App

Plot heatmap

Description

This function plots a heatmap of feature abundance.

Usage

plotHeatmap(
  aggdat,
  features = NULL,
  log = TRUE,
  sort_by = c("Fano", "MAD", "Variance"),
  nfeat = 50,
  col_by = NULL,
  row_by = NULL,
  plotTitle = ""
)

Arguments

aggdat	aggregated MRExperiment
features	Vector of features to plot. If NULL, the top 'nfeat' features in terms of 'sort_by' will be plotted.
log	Log2 transform data. Default is TRUE.
sort_by	Dispersion measure to sort features, one of "Fano", "MAD", and "Variance"
nfeat	Number of features to display. Default is 50.
col_by	Vector of phenotypes for coloring.
row_by	Name of feature level for coloring.
plotTitle	Plot title. By default, no title.

Value

plotly heatmap

Examples

data("mouseData", package = "metagenomeSeq")
aggdat <- aggFeatures(mouseData, level = "genus")
plotHeatmap(aggdat, sort_by = "Fano")

zoecastillo/microbiomeExplorer documentation built on Sept. 11, 2022, 7:40 a.m.