peak_Profile_Heatmap: peak_Profile_Heatmap

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

peak_Profile_Heatmap

Description

plot peak heatmap and profile in a picture

Usage

peak_Profile_Heatmap(
  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_name = NULL,
  ncol = NULL,
  nrow = NULL,
  facet_label_text_size = 12,
  conf,
  facet = "row",
  free_y = TRUE,
  height_proportion = 4
)

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_name	the name for each window, which will also be showed in the picture as labels
ncol	the ncol of plotting a list of peak
nrow	the nrow of plotting a list of peak
facet_label_text_size	the size of facet label text
conf	confidence interval
facet	one of 'none', 'row' and 'column'
free_y	if TRUE, y will be scaled by AvgProf
height_proportion	the proportion of profiling picture and heatmap

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