plotTSSEnrichment: Plot a TSS Enrichment Plot for Each Sample

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

Plot a TSS Enrichment Plot for Each Sample

Description

This function will plot a TSS enrichment plot for each sample. Cells in ArchRProject are the only ones used when making this plot.

Usage

plotTSSEnrichment(
  ArchRProj = NULL,
  groupBy = "Sample",
  chromSizes = getChromSizes(ArchRProj),
  TSS = getTSS(ArchRProj),
  flank = 2000,
  norm = 100,
  smooth = 11,
  pal = NULL,
  returnDF = FALSE,
  threads = getArchRThreads(),
  logFile = createLogFile("plotTSSEnrichment")
)

Arguments

ArchRProj	An ArchRProject object.
groupBy	The name of the column in cellColData to use for grouping cells together for summarizing.
chromSizes	A GRanges object of the chromosome lengths. See getChromSizes for more info.
TSS	A GRanges object containing the locations of stranded TSS regions. The default behavior is to try to retrieve this information from the geneAnnotation stored in the ArchRProject.
flank	An integer that specifies how far in bp (+/-) to extend the TSS for plotting.
norm	An integer that specifies the number of base pairs from the ends of the flanks to be used for normalization. For example if flank=2000 and norm=100, the TSS insertions will be normalized by +/- 1900-2000 bp from the TSS.
smooth	An integer that indicates the smoothing window (in basepairs) to be applied to the TSS plot.
pal	A color palette representing the groups from groupBy in TSS plot.
returnDF	A boolean value that indicates whether to return a data.frame containing the plot information instead of plotting the TSS enrichment plot.
threads	An integer specifying the number of threads to use for calculation. By default this uses the number of threads set by addArchRThreads().
logFile	The path to a file to be used for logging ArchR output.

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Plot TSS
p <- plotTSSEnrichment(proj, groupBy = "Clusters")

# PDF
plotPDF(p, name = "TSS-Enrich", ArchRProj = proj)

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