Plot copy number heatmap

Heatmap reflecting the magnitude of estimated copy numbers relative to some pre-defined limits. Estimates may be obtained using pcf or multipcf, and results may be visualized over the entire genome or by chromosomes.

Usage

plotHeatmap(
  segments,
  upper.lim,
  lower.lim = -upper.lim,
  pos.unit = "bp",
  chrom = NULL,
  layout = c(1, 1),
  ...
)

Arguments

segments

a data frame containing the segmentation results found by either pcf() or multipcf().

upper.lim

a positive numeric vector giving the upper limits(s) to be applied. The colors in the heatmap will reflect the magnitude of the estimated copy numbers relative to this limit, see details.

lower.lim

a negative numeric vector of same length as upper.lim giving the lower limits(s) to be applied. Default is to use the negative value of upper.lim.

pos.unit

the unit used to represent the probe positions. Allowed options are "mbp" (mega base pairs), "kbp" (kilo base pairs) or "bp" (base pairs). By default assumed to be "bp".

chrom

a numeric or character vector with chromosome number(s) to indicate which chromosome(s) is (are) to be plotted. If unspecified the whole genome is plotted.

layout

the vector of length two giving the number of rows and columns in the plot window. Default is c(1,1).

...

other optional graphical parameters. These include the plot arguments xlab, ylab, main, cex.main, mgp, cex.lab, cex.axis, mar and title (see par() on these), as well as plot.size, plot.unit, plot.ideo, ideo.frac, cyto.text, assembly and cex.cytotext (see plotSample() on these). In addition, a range of graphical arguments specific for this plot function may be specified:

colors

a character vector of length three giving the colors to interpolate in the heatmap, default is c("dodgerblue","black","red").

n.col

an integer giving the number of color shades to be applied in the interpolation, default is 50.

sample.labels

a logical value indicating whether sample labels are to be plotted along the y-axis. Default is TRUE.

sep.samples

a number in the range 0 to 0.4 used to create some space between samples. Default is 0, which implies that there is no space.

sample.line

a numeric scalar giving the margin line where the sample labels should be written, starting at 0 counting outwards. Default is 0.2.

sample.cex

the size of the sample labels.

Details

For each sample, the segments are represented by a rectangle plotted in a color corresponding to the difference between the segment copy number value and the limits. If the value is below lower.lim, the color of the rectangle will equal the input in colors[1] (default dodgerblue). If the value is above lower.lim, but below zero, the color of the rectangle will be a nuance between the input in colors[1] and colors[2] (default black). The closer the value is to zero, the closer the nuance will be to colors[2]. Similary, if the value is above upper.lim, the color of the rectangle will equal the input in colors[3] (default red), whereas if the value is below upper.lim, but above zero, the color will be a nuance between the input in colors[2] and colors[3]. Again, the closer the value is to zero, the closer the nuance will be to colors[2].

Each row in the heatmap represents a sample, while probe positions are reflected along the x-axis.

Note

This function applies par(fig), and is therefore not compatible with other setups for arranging multiple plots in one device such as par(mfrow,mfcol).

Author

Gro Nilsen

Examples

#Load lymphoma data
data(lymphoma)

#Run pcf to obtain estimated copy number values
seg <- pcf(data=lymphoma,gamma=12)
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 1q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 3p 
#> pcf finished for chromosome arm 3q 
#> pcf finished for chromosome arm 4p 
#> pcf finished for chromosome arm 4q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7p 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm 10p 
#> pcf finished for chromosome arm 10q 
#> pcf finished for chromosome arm 11p 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 12q 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16p 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 18p 
#> pcf finished for chromosome arm 18q 
#> pcf finished for chromosome arm 19p 
#> pcf finished for chromosome arm 19q 
#> pcf finished for chromosome arm 20p 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 21q 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 23p 
#> pcf finished for chromosome arm 23q 

#Heatmap for entire genome, two limit values:
plotHeatmap(segments=seg,upper.lim=c(0.1,0.5),layout=c(2,1))


#Heatmap for the first 4 chromosomes:
plotHeatmap(segments=seg,upper.lim=0.1,chrom=c(1:4),layout=c(2,2))