plotDistToTSS.data.frame: plotDistToTSS.data.frame

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

plotDistToTSS.data.frame

Description

plot feature distribution based on the distances to the TSS

Usage

plotDistToTSS.data.frame(
  peakDist,
  distanceColumn = "distanceToTSS",
  distanceBreaks = c(0, 1000, 3000, 5000, 10000, 1e+05),
  palette = NULL,
  xlab = "",
  ylab = "Binding sites (%) (5'->3')",
  title = "Distribution of transcription factor-binding loci relative to TSS",
  categoryColumn = ".id"
)

Arguments

peakDist	peak annotation
distanceColumn	column name of the distance from peak to nearest gene
distanceBreaks	default is 'c(0, 1000, 3000, 5000, 10000, 100000)'
palette	palette name for coloring different distances. Run 'RColorBrewer::display.brewer.all()' to see all applicable values.
xlab	x label
ylab	y lable
title	figure title
categoryColumn	category column, default is ".id"

Value

bar plot that summarize distance from peak to TSS of the nearest gene.

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

See Also

annotatePeak

Examples

## Not run: 
require(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
peakfile <- system.file("extdata", "sample_peaks.txt", package="ChIPseeker")
peakAnno <- annotatePeak(peakfile, TxDb=txdb)
plotDistToTSS(peakAnno)

## End(Not run)

YuLab-SMU/ChIPseeker documentation built on Nov. 2, 2024, 1:45 p.m.