Plot enrichment as heatmap

Creates a heatmap summarizing the enrichment of each gene-set cluster in each source (useful for datasets with many data sources).

Usage

plotHeatmap(
  geneSetsList,
  resolution = NULL,
  plotFrom = c("nlog10pval", "enrichment_score"),
  summaryStat = c("median", "max", "mean"),
  removeClusterId = FALSE,
  highlightClusterNo = NULL,
  transpose = FALSE,
  cutree_rows = NA,
  cutree_cols = NA,
  drawPlot = TRUE,
  scaleCols = "auto"
)

Arguments

geneSetsList

'gsList' object with clusters and labels.

resolution

The cluster resolution to plot. Default NULL uses the active resolution: the optimal resolution found by clusterGeneSets(), or the one last set with updateResolution() or updateClusterLabels().

plotFrom

Name of the column of the 'enrichmentScore' slot to visualize, e.g. 'nlog10pval' or 'enrichment_score'. Only numeric columns that are annotated (i.e. not all NA) can be plotted - which columns are available depends on what was supplied to 'geneSetsDF' in 'initializeList()'. Only one column is plotted; if several are supplied the first plottable one is used (the default therefore falls back to 'enrichment_score' when no p-values were supplied).

summaryStat

How the values of the gene sets within a cluster are summarized into the value shown in each heatmap cell. One of 'median' (default), 'max' or 'mean'. Note that 'max' is the largest signed value, so for signed scores (e.g. NES) a strongly negative cluster will be summarized by its least negative gene set.

removeClusterId

Logical, if TRUE the cluster number will be removed from each cluster label. Default: FALSE.

highlightClusterNo

A vector with the cluster numbers of the clusters (at the resolution) to highlight (in bold) in the plot.

transpose

A logical indicating whether to transpose the heatmap (switch rows and cols)

cutree_rows

pheatmap control parameter. Number of clusters the rows are divided into

cutree_cols

pheatmap control parameter. Number of clusters the columns are divided into

drawPlot

Whether to draw the plot. Default to TRUE.

scaleCols

Whether to z-score each cluster across the sources before plotting. One of "auto" (default), TRUE or FALSE. "auto" scales only when there are at least three sources: with one source there is nothing to compare, and with two sources the z-scores can only be -0.71, 0 or 0.71. Scaling is always across sources, also when transpose = TRUE.

Value

The pheatmap object, invisibly. Use drawPlot = FALSE to get it without drawing, e.g. to arrange it with other plots.

Details

Cells of clusters that have no gene set from a source are shown in gray. Rows and columns are ordered by hierarchical clustering when there are at least two sources (absent cells count as 0 for the clustering).

Examples

plotHeatmap(exampleGsList)

plotHeatmap(exampleGsList, plotFrom = 'enrichment_score', summaryStat = 'mean')