genomeChrPlot {DiNAMIC.Duo}

A Function for Plotting Mean Copy Number Values and Differences Across Multiple Chromosomes

Description

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

Usage

genomeChrPlot(
  inputList,
  plottingChrs = NULL,
  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,
  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.

plottingChrs

A numeric list of chromosomes to be plotted. A separate plot is produced for each chromosome.

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").

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.

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 in the 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

Although genomePlot can be used to visualize copy number values and copy number alterations across the genome, the scale makes it difficult to see events that affect small genomic regions. These events are easier to see if the viewing window is restricted to individual chromosomes, as is done here. 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.

Value

Creates a multi-page plot of mean copy number values and differences by chromosome.

Examples

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