ATACTrack.Seurat: ATACTrack function

In CostaLab/MOJITOO: MOJITOO: (M)ulti-m(O)dal (J)oint (I)ntegra(T)ion of c(O)mp(O)nents

ATACTrack function

Description

Plot ATACTracks with top peaks

Usage

## S3 method for class '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([e-mail][, 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()

CostaLab/MOJITOO documentation built on Oct. 28, 2024, 10:42 a.m.