smooth.region.plot {MVisAGe}

A Function for Plotting Smoothed Pearson Correlation Coefficients Genomewide

Description

This function plots smoothed R or R^2 values produced by corr.list.compute() genomewide.

Usage

smooth.region.plot(plot.list, plot.chr, plot.start, plot.stop,
  plot.column = "R^2", annot.colors = c("black", "red", "green", "blue",
  "cyan"), vert.pad = 0.05, ylim.low = NULL, ylim.high = NULL,
  plot.legend = TRUE, legend.loc = "topleft", lty.vec = NULL,
  lwd.vec = NULL, loess.span = 50, expand.size = 50,
  xaxis.label = "Position (Mb)", yaxis.label = NULL, main.label = NULL,
  axis.cex = 1, label.cex = 1, xaxis.line = 1.5, yaxis.line = 2.5,
  main.line = 0)

Arguments

plot.list

A list produced by corr.list.compute().

plot.chr

The chromosome for which gene-level R or R^2 values will be plotted.

plot.start

The genomic position (in base pairs) where the plot will start.

plot.stop

The genomic position (in base pairs) where the plot will stop.

plot.column

"R" or "R^2" depending on whether Pearson correlation coefficients or squared Pearson correlation coefficients will be plotted. Default = "R^2".

annot.colors

A vector of colors used for plotting values in different entries of plot.list. Default = c("black", "red", "green", "blue", "cyan").

vert.pad

Amount of vertical white space in the plot. Default = 0.

ylim.low

Smallest value on the y-axis (used to control the range of values on the y-axis). Default = NULL.

ylim.high

Largest value on the y-axis (used to control the range of values on the y-axis). Default = NULL.

plot.legend

Logical value specifying whether a legend should be included. Default = FALSE.

legend.loc

Character value specifing the location of the legend. Default = "topright". See See legend.

lty.vec

Vector specifying line types for plotting values in different entries of plot.list. Default = NULL. See par.

lwd.vec

Vector specifying line widths for plotting values in different entries of plot.list. Default = NULL. See par.

loess.span

A numerical value used to control the level of smoothing. Smoothing is performed separately for each chromosome, and loess.span effectively defines the number of genes in each smoothing window. Default = 250.

expand.size

A numerical value used to control smoothing at the ends of the region of interest. Both ends of the region are artificially extended by expand.size genes, smoothing is performed on the expanded region, and then the smoothed values are restricted to the size of the original region. Default = 50.

xaxis.label

Text used to label the x-axis of the plot. Default = "Chromosome". See plot.

yaxis.label

Text used to label the y-axis of the plot. Default = NULL. See plot.

main.label

Text used to label the plot header. Default = NULL. See plot.

axis.cex

Numerical value used to specify the font size on the axes. Default = 1. See par.

label.cex

Numerical value used to specify the font size for the axis labels. Default = 1. See par.

xaxis.line

Numerical value used to specify location of xaxis.label. Default = 0. See mtext.

yaxis.line

Numerical value used to specify location of yaxis.label. Default = 0. See mtext.

main.line

Numerical value used to specify location of main.label. Default = 0. See mtext.

Value

Creates a plot of gene-level R or R^2 values produced by corr.list.compute().

Examples

exp.mat = tcga.exp.convert(exp.mat)

 cn.mat = tcga.cn.convert(cn.mat)

 prepped.data = data.prep(exp.mat, cn.mat, gene.annot, sample.annot, log.exp = FALSE)

 pd.exp = prepped.data[["exp"]]

 pd.cn = prepped.data[["cn"]]

 pd.ga = prepped.data[["gene.annot"]]

 pd.sa = prepped.data[["sample.annot"]]

 output.list = corr.list.compute(pd.exp, pd.cn, pd.ga, pd.sa)

 smooth.region.plot(plot.list = output.list, plot.chr = 11, plot.start = 0e6, plot.stop = 135e6)