importScSeqScore: plot tracks for single cell RNAseq

In jianhong/trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

plot tracks for single cell RNAseq

Description

Plot single cell RNAseq data as heatmap track for Seurat object.

Usage

importScSeqScore(
  object,
  files,
  samplenames,
  ...,
  txdb,
  gene,
  id,
  idents,
  gr,
  color,
  withCoverageTrack = TRUE,
  flag = scanBamFlag(isSecondaryAlignment = FALSE, isUnmappedQuery = FALSE,
    isNotPassingQualityControls = FALSE, isSupplementaryAlignment = FALSE)
)

Arguments

object	Seurat object.
files	bam file to be scanned.
samplenames	sample names for files.
...	parameters used by readGAlignmentsList or readGAlignments
txdb	TxDb object for gene model.
gene	Gene name to plot. (row value)
id	The id of gene used in txdb.
idents	indentity class to define the groups to plot. (column value)
gr	GRanges object to define the ploting region.
color	vector of colors used in heatmap.
withCoverageTrack	plot coverage track or not.
flag	An integer(2) vector used to filter reads based on their 'flag' entry.

Examples

## Not run: 
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
test_file <- "https://github.com/10XGenomics/subset-bam/raw/master/test/test.bam"
trs <- importScSeqScore(files=test_file, 
                        txdb=TxDb.Hsapiens.UCSC.hg19.knownGene,
                        id="653635", gene = "WASH7P")

## End(Not run)

jianhong/trackViewer documentation built on Dec. 10, 2024, 10:33 a.m.