unsmooth.region.plot {MVisAGe}

A Function for Plotting Pearson Correlation Coefficients in a Given Genomic Region

Description

This function plots unsmoothed R or R^2 values produced by corr.list.compute() in a specified genomic region.

Usage

unsmooth.region.plot(plot.list, plot.chr, plot.start, plot.stop,
  plot.column = "R", plot.points = TRUE, plot.lines = TRUE,
  gene.names = TRUE, annot.colors = c("black", "red", "green", "blue",
  "cyan"), vert.pad = 0.05, num.ticks = 5, ylim.low = NULL,
  ylim.high = NULL, pch.vec = NULL, lty.vec = NULL, lwd.vec = NULL,
  plot.legend = TRUE, legend.loc = "topright")

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".

plot.points

Logical value specifying whether points should be included in the plot. Default = TRUE.

plot.lines

Logical values specifying whether points should be connected by lines. Default = FALSE.

gene.names

Logical value specifying whether gene names should appear on the plot. Default = FALSE.

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 = 0.05.

num.ticks

Number of ticks on the x-axis. Default = 5.

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.

pch.vec

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

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.

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

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)

 unsmooth.region.plot(plot.list = output.list, plot.chr = 11, plot.start = 69e6, plot.stop = 70.5e6)