PlotCoverage: PlotCoverage

In VCCRI/Sierra: PolyA counting and differential transcript usage analysis for scRNA-seq data

PlotCoverage

Description

Plots read coverage across a gene for a set of BAM files and/or wig data.

Usage

PlotCoverage(
  genome_gr,
  geneSymbol = "",
  wig_data = NULL,
  bamfiles = NULL,
  peaks.annot = NULL,
  label.transcripts = FALSE,
  wig_same_strand = TRUE,
  genome = NULL,
  pdf_output = FALSE,
  wig_data.tracknames = NULL,
  bamfile.tracknames = NULL,
  output_file_name = "",
  zoom_3UTR = FALSE,
  annotation.fontsize = NULL,
  axis.fontsize = NULL,
  ylims = NULL
)

Arguments

genome_gr	: genome granges object
geneSymbol	: Name of gene symbol
wig_data	can be a data frame or a genomic ranges object. Must be stranded.
bamfiles	: BAM filenames that are to be displayed as data tracks
peaks.annot	an optionally named vector of peaks to annotate on the plot.
label.transcripts	if set to TRUE, adds transcript identifiers to the gene model
wig_same_strand	Display same strand or opposing strand of wig data (compared to reference gene)
genome	: genome object
pdf_output	: If true will create output pdf files
wig_data.tracknames	: WIG track display names. Assumed to be in same order as wig_data.
bamfile.tracknames	: BAM track display names. Assumed to be in same order as bamfiles.
output_file_name	: Used if pdf_output is true. Location of where files will be placed.
zoom_3UTR	: If TRUE will create a second figure which will zoom in on 3'UTR.
annotation.fontsize	font size for optional peak and transcript annotations
axis.fontsize	font size for the axis labels
ylims	manually set the y-axis scale

Value

NULL by default.

Examples

extdata_path <- system.file("extdata",package = "Sierra")
reference.file <- paste0(extdata_path,"/Vignette_cellranger_genes_subset.gtf")
gtf_gr <- rtracklayer::import(reference.file)
bam.files <- c(paste0(extdata_path,"/Vignette_example_TIP_mi.bam"),
                 paste0(extdata_path,"/Vignette_example_TIP_sham.bam"))


PlotCoverage(genome_gr = gtf_gr, geneSymbol = "Lrrc58", genome = "mm10", 
           bamfiles = bam.files, bamfile.tracknames=c("MI", "sham"))
           
## Alternatively, plot with annotated peaks
peaks.annot <- c("Lrrc58:16:37888444-37888858:1", "Lrrc58:16:37883336-37883588:1")
names(peaks.annot) <- c("Peak 1", "Peak 2")

PlotCoverage(genome_gr = gtf_gr, geneSymbol = "Lrrc58", genome = "mm10", 
          peaks.annot = peaks.annot, bamfiles = bam.files, 
          bamfile.tracknames=c("MI", "sham"))

VCCRI/Sierra documentation built on July 3, 2023, 6:39 a.m.