peakHeatmap: peakHeatmap

In YuLab-SMU/ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

peakHeatmap

Description

plot the heatmap of peaks

Usage

peakHeatmap(
  peak,
  weightCol = NULL,
  TxDb = NULL,
  upstream = 1000,
  downstream = 1000,
  xlab = "",
  ylab = "",
  title = NULL,
  palette = NULL,
  verbose = TRUE,
  by = "gene",
  type = "start_site",
  nbin = NULL,
  ignore_strand = FALSE,
  windows,
  ncol = NULL,
  nrow = NULL
)

Arguments

peak	peak file or GRanges object
weightCol	column name of weight
TxDb	TxDb object
upstream	upstream position
downstream	downstream position
xlab	xlab
ylab	ylab
title	title
palette	palette to be filled in,details see scale_colour_brewer
verbose	print message or not
by	one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'
type	one of "start_site", "end_site", "body"
nbin	the amount of nbines
ignore_strand	ignore the strand information or not
windows	a collection of region
ncol	the ncol of plotting a list of peak
nrow	the nrow of plotting a list of peak

Value

figure

Author(s)

G Yu

YuLab-SMU/ChIPseeker documentation built on Feb. 11, 2024, 5:22 p.m.