plotHeatmap: Plot heatmap

Description Usage Arguments Value Examples

View source: R/inter_functions.R

Description

This function plots a heatmap of feature abundance.

Usage

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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

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

microbiomeExplorer documentation built on Nov. 8, 2020, 8:16 p.m.