unsmooth.region.plot: A Function for Plotting Pearson Correlation Coefficients in a...
In MVisAGe: Compute and Visualize Bivariate Associations

Description Usage Arguments Value Examples

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

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")

`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`

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

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)