importScSeqScore {trackViewer} | R Documentation

## 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)

[Package trackViewer version 1.28.1 Index]