ATACTrack function — ATACTrack.Seurat • MOJITOO

Plot ATACTracks with top peaks

Usage

# S3 method for Seurat
ATACTrack(
  object,
  CC = 1,
  group.by = "celltype",
  bigwig.file.list = list(),
  MOJITOO.reduction = "MOJITOO",
  Peak.assay = "Peaks",
  Peaks = NULL,
  gene.model = NULL,
  cols = (ggsci::pal_igv())(51),
  ylim.datatrack = c(0, 16),
  fontsize.geneAxis = 5,
  fontsize.geneRegion = 10,
  fontsize.datatrack = 8,
  show.legend = T,
  genome = "hg38"
)

Arguments

object: Seurat object
CC: CC index to use which MOJITOO CC
group.by: data tracks group.by meta.data slot
bigwig.file.list: named list of bigwig file paths, keys should be the same as unique(object@meta.data[, group.by])
MOJITOO.reduction: MOJITOO reduction name
Peak.assay: Peak assay name
Peaks: peaks to display, will use CC top 2 positive&negative peaks if NULL
gene.model: a valid gene model object that GeneRegionTrack accept, will not display if NULL
cols: colors to show data tracks
show.legend: if show legend
genome: hg19 h38 mm9 mm10

Value

A grid.gTree, use grid.draw to plot

Examples

ATACTrack()
#> Error in ATACTrack(): argument "object" is missing, with no default