plotEnrichHeatmap: Plot a Heatmap of Peak Annotation Hypergeometric Enrichment...
In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

plotEnrichHeatmap

R Documentation

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

Description

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

Usage

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.

Examples


# Get Test ArchR Project
proj <- getTestProject()

# Get Markers
seMarker <- getMarkerFeatures(
  ArchRProj = proj, 
  useMatrix = "PeakMatrix", 
  testMethod = "binomial", 
  binarize = TRUE
)

# Get Peak Annotation Enrichment
annoEnrich <- peakAnnoEnrichment(
  seMarker = seMarker, 
  ArchRProj = proj,
  cutOff = "FDR <= 0.1 & Log2FC >= 0"
)

# Multiply by 50 since this is a super small test sample
assay(annoEnrich) <- assay(annoEnrich) * 50

#Plot
p <- plotEnrichHeatmap(annoEnrich)

#PDF
plotPDF(p, name = "PeakAnnoEnrich", ArchRProj = proj)

GreenleafLab/ArchR documentation built on Feb. 21, 2025, 3:05 p.m.