plotPeakProf: plotPeakProf_MultiWindows

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

plotPeakProf_MultiWindows

Description

plot the profile of peaks ' plotPeakProf_MultiWindows() is almost the same as plotPeakProf2(), having the main difference of accepting two or more granges objects. Accepting more granges objects can help compare the same peaks in different windows.

Usage

plotPeakProf(
  tagMatrix = NULL,
  peak,
  upstream,
  downstream,
  conf,
  by,
  type,
  windows_name = NULL,
  weightCol = NULL,
  TxDb = NULL,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  facet = "row",
  free_y = TRUE,
  verbose = TRUE,
  nbin = NULL,
  ignore_strand = FALSE,
  ...
)

Arguments

tagMatrix	tagMatrix or a list of tagMatrix
peak	peak file or GRanges object
upstream	upstream position
downstream	downstream position
conf	confidence interval
by	feature of interest
type	one of "start_site", "end_site", "body"
windows_name	the name for each window, which will also be showed in the picture as labels
weightCol	column name of weight
TxDb	TxDb object or self-made granges objects
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 bines
ignore_strand	ignore the strand information or not
...	additional parameter

Details

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.

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 value. Details see https://github.com/YuLab-SMU/ChIPseeker/issues/15

nbin refers to the number of bins. getTagMatrix() provide a binning method to get the tag matrix.

There are two ways input a list of window.

(1) Users can input a list of self-made granges objects

(2) Users can input a list of by and only one type. In this way, plotPeakProf_MultiWindows() can made a list of window from txdb object based on by and type.

Warning:

(1) All of these window should be the same type. It means users can only compare a list of "start site"/"end site"/"body region" with the same upstream and downstream.

(2) So it will be only one type and several by.

(3) Users can make window by txdb object or self-made granges object. Users can only choose one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR' or 'UTR' in the way of using txdb object. User can input any by in the way of using self-made granges object.

(4) Users can mingle the by designed for the two ways. plotPeakProf_MultiWindows can accpet the hybrid by. But the above rules should be followed.

https://github.com/YuLab-SMU/ChIPseeker/issues/189

Value

ggplot object

GuangchuangYu/ChIPseeker documentation built on Oct. 31, 2024, 9:13 a.m.