genomePlot: A Function for Plotting Mean Copy Number Values and...

Description Usage Arguments Value Examples

View source: R/genomePlot.R

Description

This function plots mean copy number values from one or two cohorts at a common set of markers across the genome.

Usage

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genomePlot(
  inputList,
  lwdVec = rep(1, 3),
  ltyVec = c(1:3),
  lineColorVec = c("red", "blue", "black"),
  ylimLow = -1,
  ylimHigh = 1,
  chrLabel = TRUE,
  xaxisLabel = "Chromosome",
  yaxisLabel = NULL,
  mainLabel = NULL,
  rectColors = c("light gray", "gray"),
  axisCex = 1,
  labelCex = 1,
  xaxisLine = 2.5,
  yaxisLine = 2.5,
  mainLine = 0,
  marginVec = c(4, 4, 3, 3),
  legendText = NULL,
  highThreshold = NULL,
  lowThreshold = NULL,
  showLegend = FALSE,
  legendXQuantile = 0.55,
  legendYCoord = 1
)

Arguments

inputList

A list produced by dataPrep.

lwdVec

A vector of line widths. Default = rep(1, 3). See par.

ltyVec

A vector of line types. Default = c(1:3). See par.

lineColorVec

A vector of line colors. Default = c("red", "blue", "black"). See par.

ylimLow

The lower limit of the y-values in the plot. Default = -1. See plot.

ylimHigh

The upper limit of the y-values in the plot. Default = 1. See plot.

chrLabel

Binary value determining whether or not chromosomes are labeled. Default = TRUE.

xaxisLabel

Label for the x-axis in the plot. Default = "Chromosome". See plot.

yaxisLabel

Label for the y-axis in the plot. Default = NULL. See plot.

mainLabel

Main label in the plot. Default = NULL. See plot.

rectColors

Background colors for different chromosomes. Default = c("light gray", "gray").

axisCex

Point size for the scale on the axis. Default = 1. See par.

labelCex

Point size for the axis label. Default = 1. See par.

xaxisLine

Numerical value used to specify the location of the x-axis label. Default = 2.5. See mtext.

yaxisLine

Numerical value used to specify the location of the y-axis label. Default = 2.5. See mtext.

mainLine

Numerical value used to specify the location of the main.label. Default = 0. See mtext.

marginVec

Numerical vector specifying margin sizes. Default = c(4, 4, 3, 3). See par.

legendText

Character vector used to legend. Only shown if showLegend = TRUE. Default = NULL. See legend.

highThreshold

Numerical value representing the position of the upper horizontal line. Default = NULL.

lowThreshold

Numerical value representing the position of the lower horizontal line. Default = NULL.

showLegend

Binary value determining whether or not the legend is shown. Default = FALSE. See legend.

legendXQuantile

Quantile to specify the "x" location of the legend. Only relevant if showLegend = TRUE Default = 0.55. See legend.

legendYCoord

Numerical value to specify the "y"location of the legend. Only relevant if showLegend = TRUE. Default = 1. See legend.

Value

Creates a genomewide plot of mean copy number values and differences.

Examples

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genomeChrPlot(inputList = pD, ylimLow = -1.4, ylimHigh = 1.4)

DiNAMIC.Duo documentation built on Oct. 1, 2021, 1:08 a.m.