plotTSSEnrichment: Plot a TSS Enrichment Plot for Each Sample
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

plotTSSEnrichment

R Documentation

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.