plotMetaGene: Make a custom metagene plot

In kevincjnixon/ChIPATAC: Wrapper functions for useful genomic analyses like ChIP-seq or ATAC-seq.

Make a custom metagene plot

Description

Make a custom metagene plot

Usage

plotMetaGene(
  metaList,
  samples = NULL,
  subgenes = NULL,
  title = "",
  cols = NULL,
  marks = c("-500", "TSS", "TTS", "+2000"),
  xlab = "Position (bp)",
  ylab = "Occupancy",
  pal = "Dark2",
  lty = NULL,
  a = 100,
  b = 100,
  scale = F,
  retDat = F
)

Arguments

metaList	metaList object output from makeCovList(), addSym(), or scaleMeta()
samples	character vector indicating the names of the samples in metaList$cov to plot. NULL plots all.
subgenes	Character vector of gene symbols to subset coverage matrices by. Must provide gene symbols to metaList after 'addSym()' has been used.
title	Character indicating the title of the plot
cols	Numeric vector of length 3 or 4. Length 3 indicates computeMatrix run with reference-point, length 4 indicates computeMatrix run with scale-regions. Leave NULL to use suggested cols paramters from metaList. Replace to override manually. This will affect any scaling (if indicated) and will affect the placement of the markers on the x-axis.
marks	Character vector of length (length(cols)) indicating how landmarks should be labeled on the x-axis. Defaults to c("-500","TSS","TTS","+2000")
xlab	Character for x-axis label. Default is "Position (bp)"
ylab	Character for y-axis label. Default is "Occupancy".
pal	Character indicating RColourBrewer palette name for colour schemes or custom character vector containing either colour names, hexadecimal or rgb() values.
lty	Numeric indicating the line type for each sample. Default is NULL (lty=1 for each sample - solid line)
a	numeric indicating the number of columns downstream region (cols[3]-cols[4]) should be scaled down to, if scaling indicated
b	numeric indicating the number of columns upstream region (cols[1]-cols[2]) should be scaled down to, if scaling indicated
scale	Boolean indicating if up/downstream regions should be scaled. Default is FALSE. If set to TRUE, must be on computeMatrix output from scale-regions, and cols must be length 4.
retDat	Indicating which type of data should be returned. Default NULL returns no data. Logical TRUE returns data for a metagene plot. "box" returns data for boxplots of coverage.

Value

Custom metagene figure

kevincjnixon/ChIPATAC documentation built on May 25, 2023, 9:33 p.m.