GenVisR (version 1.0.4)

cnView: Construct copy-number single sample plot

Description

Given a data frame construct a plot to display raw copy number calls for a single sample.

Usage

cnView(x, y = NULL, z = NULL, genome = "hg19", chr = "chr1", CNscale = "absolute", ideogram_txtAngle = 45, ideogram_txtSize = 5, plotLayer = NULL, ideogramLayer = NULL, out = "plot")

Arguments

x

Object of class data frame with rows representing copy number calls from a single sample. The data frame must contain columns with the following names "chromosome", "coordinate", "cn", and optionally "p_value" (see details).

y

Object of class data frame with rows representing cytogenetic bands for a chromosome. The data frame must contain columns with the following names "chrom", "chromStart", "chromEnd", "name", "gieStain" for plotting the ideogram (optional: see details).

z

Object of class data frame with row representing copy number segment calls. The data frame must contain columns with the following names "chromosome", "start", "end", "segmean" (optional: see details)

genome

Character string specifying a valid UCSC genome (see details).

chr

Character string specifying which chromosome to plot one of "chr..." or "all"

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"

ideogram_txtAngle

Integer specifying the angle of cytogenetic labels on the ideogram subplot.

ideogram_txtSize

Integer specifying the size of cytogenetic labels on the ideogram subplot.

plotLayer

Valid ggplot2 layer to be added to the copy number plot.

ideogramLayer

Valid ggplot2 layer to be added to the ideogram sub-plot.

out

Character vector specifying the the object to output, one of "data", "grob", or "plot", defaults to "plot" (see returns).

Value

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

Details

cnView is able to plot in two modes specified via the `chr` parameter, these modes are single chromosome view in which an ideogram is displayed and genome view where chromosomes are faceted. For the single chromosome view cytogenetic band information is required giving the coordinate, stain, and name of each band. As a convenience cnView stores this information for the following genomes "hg19", "hg38", "mm9", "mm10", and "rn5". If the genome assembly supplied to the `genome` parameter is not one of the 5 afore mentioned genome assemblies cnView will attempt to query the UCSC MySQL database to retrieve this information. Alternatively the user can manually supply this information as a data frame to the `y` parameter, input to the `y` parameter take precedence of input to `genome`.

cnView is also able to represent p-values for copy-number calls if they are supplied via the "p_value" column in the argument supplied to x. The presence of this column in x will set a transparency value to copy-number calls with calls of less significance becoming more transparent.

If it is available cnView can plot copy-number segment calls on top of raw calls supplied to parameter `x` via the parameter `z`.

Examples

# Create data
chromosome <- 'chr14'
coordinate <- sort(sample(0:106455000, size=2000, replace=FALSE))
cn <- c(rnorm(300, mean=3, sd=.2), rnorm(700, mean=2, sd=.2), rnorm(1000, mean=3, sd=.2))
data <- as.data.frame(cbind(chromosome, coordinate, cn))

# Plot raw copy number calls
cnView(data, chr='chr14', genome='hg19', ideogram_txtSize=4)