peakHeatmap_multiple_Sets: peakHeatmap

peakHeatmap_multiple_SetsR Documentation

peakHeatmap

Description

plot the heatmap of peaks align to a sets of regions

Usage

peakHeatmap_multiple_Sets(
  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
)

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

Value

figure


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