smooth.genome.plot {MVisAGe}

A Function for Plotting Smoothed Pearson Correlation Coefficients Across Multiple Chromosomes

Description

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

Usage

smooth.genome.plot(plot.list, 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 = "bottomright",
  lty.vec = NULL, lwd.vec = NULL, loess.span = 250, expand.size = 50,
  rect.colors = c("light gray", "gray"), chr.label = TRUE,
  xaxis.label = "Chromosome", yaxis.label = NULL, main.label = NULL,
  axis.cex = 1, label.cex = 1, xaxis.line = 1.5, yaxis.line = 2.5,
  main.line = 0, margin.vec = rep(1, 4))

Arguments

plot.list

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

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 chromosomes. Both ends of each chromosome are artificially extended by expand.size genes, smoothing is performed on the expanded chromosome, and then the smoothed values are restricted to the size of the original chromosome. Default = 50.

rect.colors

A character vector of length two that controls the background color for each alternating chromosome. Default = c("light gray", "gray").

chr.label

Logical value specifying whether chromosome numbers should appear on the plot. Default = FALSE.

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 par.

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.

margin.vec

Numerical vector specifying margin sizes. Default = rep(1, 4). See par.

Value

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

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.genome.plot(plot.list = output.list, lwd.vec = c(3, 3), lty.vec = c(1, 2))