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Last data update: 2014.03.03

R: Stacked histogram plot of two different classes

plotHistTwoClasses

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))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(puma)
Loading required package: oligo
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================
Loading required package: mclust
Package 'mclust' version 5.2
Type 'citation("mclust")' for citing this R package in publications.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/puma/plotHistTwoClasses.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotHistTwoClasses
> ### Title: Stacked histogram plot of two different classes
> ### Aliases: plotHistTwoClasses
> ### Keywords: hplot
> 
> ### ** 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))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>