PlotCoverageByCell: Plot raw count signal from scATACseq data per cell in heatmap

In crazyhottommy/scATACutils: What the Package Does (One Line, Title Case)

Description

Plot raw count signal from scATACseq data per cell in heatmap

Usage

PlotCoverageByCell(chrom = NULL, start = NULL, end = NULL, gene_name,
  upstream = 2000, downstream = 2000, fragment, barcodeList,
  genome = "hg19", txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
  eg.db = org.Hs.eg.db, cutSite = FALSE, col_fun = c("white", "blue",
  "red"))

Arguments

chrom	chromosome
start	start
end	end
gene_name	the name of the gene to plot
upstream	upstream bp to include
downstream	downstream bp to include
fragment	the fragment.tsv.gz file from 10x cellranger output
barcodeList	a vector of valid cell barcode to include
genome	hg19, hg38 or mm9, mm10
txdb	a transcriptdb object. e.g.TxDb.Hsapiens.UCSC.hg19.knownGene
eg.db	an orgdb object e.g.org.Hs.eg.db
cutSite	whether use the cut sites instead of the whole fragmeng. Default FALSE
col_fun	color of the corresponding count for c(0,1,2). e.g. c("white", "blue", "red")

Value

A complexHeatmap

Examples

## Not run: 
library(readr)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
barcodes<- read_tsv("~/5k_pbmc_atac/pbmc_5k_atac_barcodes.tsv", col_names = FALSE)
PlotCoverageByCell(gene_name = "MS4A1",
upstream = 2000,
downstream = 8000,
fragment= "~/5k_pbmc_atac/fragments.tsv.gz",
barcodeList=barcodes$X1,
genome = "hg19",
txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
eg.db = org.Hs.eg.db, cutSite = FALSE)

## End(Not run)

crazyhottommy/scATACutils documentation built on June 15, 2020, 9:31 p.m.