rliger (version 2.0.1)

plotMarkerHeatmap: Create heatmap for showing top marker expression in conditions

Description

Create heatmap for showing top marker expression in conditions

Usage

plotMarkerHeatmap(
  object,
  result,
  topN = 5,
  lfcThresh = 1,
  padjThresh = 0.05,
  pctInThresh = 50,
  pctOutThresh = 50,
  dedupBy = c("logFC", "padj"),
  groupBy = NULL,
  groupSize = 50,
  column_title = NULL,
  ...
)

Arguments

object

A liger object, with normalized data and metadata to annotate available.

result

The data.frame returned by runMarkerDEG.

topN

Number of top features to be plot for each group. Default 5.

lfcThresh

Hard threshold on logFC value. Default 1.

padjThresh

Hard threshold on adjusted P-value. Default 0.05.

pctInThresh, pctOutThresh

Threshold on expression percentage. These mean that a feature will only pass the filter if it is expressed in more than pctInThresh percent of cells in the corresponding cluster. Similarly for pctOutThresh. Default 50 percent for both.

dedupBy

When ranking by padj and logFC and a feature is ranked as top for multiple clusters, assign this feature as the marker of a cluster when it has the largest "logFC" in the cluster or has the lowest "padj". Default "logFC".

groupBy

Cell metadata variable names for cell grouping. Downsample balancing will also be aware of this. Default c("dataset", "leiden_cluster").

groupSize

Maximum number of cells in each group to be downsampled for plotting. Default 50.

column_title

Title on the column. Default NULL.

...

Parameter passed to wrapped functions in the inheritance order: plotGeneHeatmap, .plotHeatmap, ComplexHeatmap::Heatmap

Examples

markerTable <- runMarkerDEG(pbmcPlot)
plotMarkerHeatmap(pbmcPlot, markerTable)