cnSpec: Construct copy-number cohort plot

In GenVisR: Genomic Visualizations in R

Description

Given a data frame construct a plot to display copy-number calls for a cohort of samples.

Usage

cnSpec(
  x,
  y = NULL,
  genome = "hg19",
  plot_title = NULL,
  CN_Loss_colour = "#002EB8",
  CN_Gain_colour = "#A30000",
  x_title_size = 12,
  y_title_size = 12,
  facet_lab_size = 10,
  plotLayer = NULL,
  out = "plot",
  CNscale = "absolute"
)

Arguments

x	Object of class data frame with rows representing copy-number segment calls. The data frame must contain columns with the following names "chromosome", "start", "end", "segmean", "sample".
y	Object of class data frame with rows representing chromosome boundaries for a genome assembly. The data frame must contain columns with the following names "chromosome", "start", "end" (optional: see details).
genome	Character string specifying a valid UCSC genome (see details).
plot_title	Character string specifying title to display on the plot.
CN_Loss_colour	Character string specifying the colour value of copy number losses.
CN_Gain_colour	Character string specifying the colour value of copy number gains.
x_title_size	Integer specifying the size of the x-axis title.
y_title_size	Integer specifying the size of the y-axis title.
facet_lab_size	Integer specifying the size of the faceted labels plotted.
plotLayer	Valid ggplot2 layer to be added to the plot.
out	Character vector specifying the the object to output, one of "data", "grob", or "plot", defaults to "plot" (see returns).
CNscale	Character string specifying if copy number calls supplied are relative (i.e.copy neutral == 0) or absolute (i.e. copy neutral ==2). One of "relative" or "absolute"

Details

cnSpec requires the location of chromosome boundaries for a given genome assembly in order to ensure the entire chromosome space is plotted. As a convenience this information is available to cnSpec for the following genomes "hg19", "hg38", "mm9", "mm10", "rn5" and can be retrieved by supplying one of the afore mentioned assemblies via the 'genome' parameter. If a genome assembly is supplied to the 'genome' parameter and is unrecognized cnSpec will attempt to query the UCSC MySQL database for the required information. If chromosome boundary locations are unavailable for a given assembly or if it is desireable to plot a specific region encapsulating the copy number data these boundaries can be supplied to the 'y' paramter which has priority of the parameter 'genome'.

The 'plotLayer' parameter can be used to add an additional layer to the ggplot2 graphic (see vignette).

Value

One of the following, a list of dataframes containing data to be plotted, a grob object, or a plot.

Examples

cnSpec(LucCNseg, genome="hg19")

GenVisR documentation built on Dec. 28, 2020, 2 a.m.