plotGexpProfile: Plot gene expression profile

In JEFworks/HoneyBADGER: HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data

Description

Plot gene expression profile

Usage

plotGexpProfile(gexp.norm, genes, chrs = paste0("chr", c(1:22)),
  region = NULL, window.size = 101, zlim = c(-2, 2), cellOrder = NULL,
  widths = NULL)

Arguments

gexp.norm	Normalized gene expression matrix
genes	GRanges annotation of gene names and coordinates
chrs	Chromosomes to be plotted (default: paste0('chr', c(1:22, 'X')))
region	Optional GenomicRanges region of interest such as expected CNV boundaries. (default: NULL)
window.size	Window size for sliding window mean. Must be odd number. (default: 101)
zlim	Limit for plotting heatmap (default: c(-2,2))
cellOrder	Order of cells. If 'set' will be automatically ordered by clustering. Else will be same order as input.
widths	Widths of chromosomes in plot. If 'set' will depend on number of genes in region. Else will be equal.

Examples

data(gexp)
data(ref)
require(biomaRt) ## for gene coordinates
mart.obj <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", 
    dataset = 'hsapiens_gene_ensembl', 
    host = "jul2015.archive.ensembl.org")
gexp.mats <- setGexpMats(gexp, ref, mart.obj, filter=FALSE, scale=FALSE)
##Set by known chromosome size widths:
##https://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes
gexp.plot <- plotGexpProfile(gexp.mats$gexp.norm, gexp.mats$genes, 
    widths=c(249250621, 243199373, 198022430, 191154276, 180915260, 
    171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 
    133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 
    78077248, 59128983, 63025520, 51304566, 48129895)/1e7) 

JEFworks/HoneyBADGER documentation built on July 24, 2021, 3:01 p.m.