Plot a TSS Enrichment Plot for Each Sample — plotTSSEnrichment • ArchR

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

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)