plotTSSEnrichment.Rd
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") )
ArchRProj | An |
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groupBy | The name of the column in |
chromSizes | A GRanges object of the chromosome lengths. See |
TSS | A |
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 |
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 |
threads | An integer specifying the number of threads to use for calculation. By default this uses the number of threads set by |
logFile | The path to a file to be used for logging ArchR output. |