Plot a Heatmap of Peak Annotation Hypergeometric Enrichment in Marker Peaks.

This function will plot a heatmap of hypergeometric enrichment of a given peakAnnotation within the defined marker peaks.

plotEnrichHeatmap(
  seEnrich = NULL,
  pal = paletteContinuous(set = "comet", n = 100),
  n = 10,
  cutOff = 20,
  pMax = Inf,
  clusterCols = TRUE,
  binaryClusterRows = TRUE,
  labelRows = TRUE,
  rastr = TRUE,
  transpose = FALSE,
  returnMatrix = FALSE,
  logFile = createLogFile("plotEnrichHeatmap")
)

Arguments

seEnrich	A SummarizedExperiment object containing peak enrichment information returned by peakAnnoEnrichment().
pal	A custom continuous palette (see paletteContinuous()) used to override the default continuous palette for the heatmap.
n	The number of top enriched peakAnnotations per column from the seMarker to display in the heatmap. This number can be lowered to improve visibility of the heatmap.
cutOff	A numeric cutOff that indicates the minimum P-adj enrichment to be included in the heatmap.
pMax	A numeric representing the maximum P-adj for plotting in the heatmap.
clusterCols	A boolean indicating whether or not to cluster columns in the heatmap.
binaryClusterRows	A boolean indicating whether or not to cluster rows using binary classification in the heatmap.
labelRows	A boolean indicating whether or not to label all rows in the heatmap.
rastr	A boolean value that indicates whether the plot should be rasterized using ComplexHeatmap. This does not rasterize lines and labels, just the internal portions of the plot.
transpose	A boolean determining whether to transpose the heatmap in the plot.
returnMatrix	A boolean determining whether to return the matrix corresponding to the heatmap rather than generate a plot.
logFile	The path to a file to be used for logging ArchR output.