plotPvalHist: Function plotPvalHist

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Description

Generate a facet plot (or optionally individual plots) from a dataframe of numbers. Intended to perform histogram analysis of pvalue distributions. But should be useful for any dataframe of numeric columns.

Usage

plotPvalHist(
  P.Val,
  Facet = TRUE,
  savePlot = FALSE,
  fileNames = NULL,
  binWidth = 0.02,
  baseFontSize = 12,
  facetFontSize = NULL,
  alpha = 0.6,
  color = "dodgerblue3",
  fill = "dodgerblue3"
)

Arguments

P.Val	a matrix or dataframe of numeric data; col=samples
Facet	Set to FALSE to print individual plots instead of a facetted plot. (Default = TRUE)
savePlot	TRUE saves the plot(s) to .PNG files
fileNames	Pass a single filename for a facetted plot to save the plot to a file. Pass a list of filenames if Facet=FALSE (length must equal sample count).
binWidth	Range is always 0-1 for pvalues. So this defaults to 0.02
baseFontSize	Set the base font size for the plot using theme_grey (Default=12)
facetFontSize	control font size on the individual plot headers (default=NULL). Allows for fine tuning if the theme_grey default doesn't work for you. 10 seems good for knitr output (dependant on length of your sample titles); bigger (e.g. 14) works better for PPT.
alpha	Set the transparency. (Default = 0.6)
color	Color for the histogram outline (default = "dodgerblue3")
fill	Fill color for the histogram (default = "dodgerblue3")

Value

A ggplot2 object if facet=TRUE or a list of plots if facet=FALSE. (Default = TRUE)

Author(s)

John Thompson, [e-mail]

Examples

#Print to console, all defaults
MyPvalMatrix <- extractCol(getType(myDGEobj, "topTable"), "P.Value")
plotPvalHist (MyPvalMatrix)

#Print just to a PNG with some arguments
myplot <- plotPvalHist (MyPValMatrix, savePlot = T, fileNames = "MyPlot.PNG",
               facetFontSize= 14)

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.