plotHistTwoClasses: Stacked histogram plot of two different classes

In puma: Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Description

Stacked histogram plot of two different classes

Usage

plotHistTwoClasses(
	scores
,	class1Elements
,	class2Elements
,	space=0
,	col=c("white", "grey40")
,	xlab="PPLR"
,	ylab="Number of genes"
,	ylim=NULL
,	las=0 # axis labels all perpendicular to axes
,	legend=c("non-spike-in genes", "spike-in genes")
,	inset=0.05
,	minScore=0
,	maxScore=1
,	numOfBars=20
,	main=NULL
)

Arguments

scores	A numeric vector of scores (e.g. from the output of pumaDE)
class1Elements	Boolean vector, TRUE if element is in first class
class2Elements	Boolean vector, TRUE if element is in second class
space	Numeric. x-axis distance between bars
col	Colours for the two different classes
xlab	Title for the x-axis
ylab	Title for the y-axis
ylim	2-element numeric vector showing minimum and maximum values for y-axis.
las	See par. Default of 0 means axis labels all perpendicular to axes.
legend	2-element string vector giving text to appear in legend for the two classes.
inset	See legend
minScore	Numeric. Minimum score to plot.
maxScore	Numeric. Maximum score to plot.
numOfBars	Integer. Number of bars to plot.
main	String. Main title for the plot.

Value

This function has no return value. The output is the plot created.

Author(s)

Richard D. Pearson

Examples

	class1 <- rnorm(1000,0.2,0.1)
	class2 <- rnorm(1000,0.6,0.2)
	class1[which(class1<0)] <- 0
	class1[which(class1>1)] <- 1
	class2[which(class2<0)] <- 0
	class2[which(class2>1)] <- 1
	scores <- c(class1, class2)
	class1elts <- c(rep(TRUE,1000), rep(FALSE,1000))
	class2elts <- c(rep(FALSE,1000), rep(TRUE,1000))
	plotHistTwoClasses(scores, class1elts, class2elts, ylim=c(0,300))

puma documentation built on Nov. 8, 2020, 11:08 p.m.