plotPeakProf2: plotPeakProf2

In GuangchuangYu/ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

plotPeakProf2

Description

plot the profile of peaks automatically

Usage

plotPeakProf2(
  peak,
  upstream,
  downstream,
  conf,
  by,
  type,
  weightCol = NULL,
  TxDb = NULL,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  facet = "none",
  free_y = TRUE,
  verbose = TRUE,
  nbin = NULL,
  ignore_strand = FALSE,
  ...
)

Arguments

peak	peak file or GRanges object
upstream	upstream position
downstream	downstream position
conf	confidence interval
by	e.g. 'gene', 'transcript', 'exon' or features of interest(e.g. "enhancer")
type	one of "start_site", "end_site", "body"
weightCol	column name of weight
TxDb	TxDb object, or self-made granges object
xlab	xlab
ylab	ylab
facet	one of 'none', 'row' and 'column'
free_y	if TRUE, y will be scaled by AvgProf
verbose	print message or not
nbin	the amount of nbines
ignore_strand	ignore the strand information or not
...	additional parameter

Details

peak stands for the peak file.

by the features of interest.

(1) if users use txdb, by can be one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'. These features can be obtained by functions from txdb object.

(2) if users use self-made granges object, by can be everything. Because this by will not pass to functions to get features, which is different from the case of using txdb object. This by is only used to made labels showed in picture.

type means the property of the region. one of the "start site", "end site" and "body".

upstream and downstream parameter have different usages:

(1) if type == 'body', upstream and downstream can use to extend the flank of body region.

(2) if type == 'start_site'/'end_site', upstream and downstream refer to the upstream and downstream of the start_site or the end_site.

weightCol refers to column in peak file. This column acts as a weight vaule. Details see https://github.com/YuLab-SMU/ChIPseeker/issues/15

nbin refers to the number of bins, providing a binning method to get the tag matrix.

TxDb parameter can accept txdb object. But many regions can not be obtained by txdb object. In this case, Users can provide self-made granges served the same role as txdb object and pass to TxDb object.

plotPeakProf2() is different from the plotPeakProf(). plotPeakProf2() do not need to provide window parameter, which means plotPeakProf2() will call relevent functions to make window automatically.

Value

ggplot object

Author(s)

G Yu, Ming Li

GuangchuangYu/ChIPseeker documentation built on Feb. 9, 2024, 2:06 a.m.