plotHeatmap {microbiomeExplorer} | R Documentation

## 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")

[Package microbiomeExplorer version 1.4.0 Index]