genomePlot: A Function for Plotting Mean Copy Number Values and Differences Across the Genome

Description

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

Usage

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
)

Value

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

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 (line) of the x-axis label. Default = 2.5. See mtext.
yaxisLine: Numerical value used to specify the location (line) of the y-axis label. Default = 2.5. See mtext.
mainLine: Numerical value used to specify the location (line) 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, e.g., a threshold for assessing statistical significance. Default = NULL.
lowThreshold: Numerical value representing the position of the lower horizontal line, e.g., a threshold for assessing statistical significance. 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.

Details

This function is used to visualize copy number values and copy number alterations across the genome. If Y = NULL in the input list, then the plot shows a single line corresponding to the mean DNA copy number values based on the entries in X. If both X and Y are specified, the plot shows three lines corresponding to the mean DNA copy number values in X, the mean DNA copy number values in Y, and the difference of the mean DNA copy number values.

Examples

Run this code

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

Run the code above in your browser using DataLab