Plot the enrichment around TSS — TSSPlot • Signac

Plot the normalized TSS enrichment score at each position relative to the TSS. Requires that TSSEnrichment has already been run on the assay.

TSSPlot(object, assay = NULL, group.by = NULL, idents = NULL)

Arguments

object	A Seurat object
assay	Name of the assay to use. Should have the TSS enrichment information for each cell already computed by running `TSSEnrichment`
group.by	Set of identities to group cells by
idents	Set of identities to include in the plot

Value

Returns a ggplot2 object

Examples

if (FALSE) {
# create granges object with TSS positions
library(EnsDb.Hsapiens.v75)
gene.ranges <- genes(EnsDb.Hsapiens.v75)
gene.ranges <- gene.ranges[gene.ranges$gene_biotype == 'protein_coding', ]
tss.ranges <- GRanges(
  seqnames = seqnames(gene.ranges),
  ranges = IRanges(start = start(gene.ranges), width = 2),
  strand = strand(gene.ranges)
)
seqlevelsStyle(tss.ranges) <- 'UCSC'
tss.ranges <- keepStandardChromosomes(tss.ranges, pruning.mode = 'coarse')

# to save time use the first 2000 TSSs
atac_small <- TSSEnrichment(
object = atac_small,
tss.positions = tss.ranges[1:2000]
)
TSSPlot(atac_small)
}