puma (version 3.14.0)

plotHistTwoClasses: Stacked histogram plot of two different classes

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.

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))