plotHistTwoClasses {puma}R Documentation

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.

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))

[Package puma version 1.8.1 Index]