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Last data update: 2014.03.03

R: Basic plot of binned vectors.

plotBubble

R Documentation

Basic plot of binned vectors.

Description

This function plots takes two vectors, calculates the contingency table and plots circles sized by the contingency table value. Optional significance vectors of the values significant will shade the circles by proportion of significance.

Usage

plotBubble(yvector, xvector, sigvector = NULL, nbreaks = 10,
  ybreak = quantile(yvector, p = seq(0, 1, length.out = nbreaks)),
  xbreak = quantile(xvector, p = seq(0, 1, length.out = nbreaks)),
  scale = 1, local = FALSE, ...)

Arguments

`yvector`	A vector of values represented along y-axis.
`xvector`	A vector of values represented along x-axis.
`sigvector`	A vector of the names of significant features (names should match x/yvector).
`nbreaks`	Number of bins to break yvector and xvector into.
`ybreak`	The values to break the yvector at.
`xbreak`	The values to break the xvector at.
`scale`	Scaling of circle bin sizes.
`local`	Boolean to shade by signficant bin numbers (TRUE) or overall proportion (FALSE).
`...`	Additional plot arguments.

Value

A matrix of features along rows, and the group membership along columns.

Examples


data(mouseData)
mouseData = mouseData[which(rowSums(mouseData)>139),]
sparsity = rowMeans(MRcounts(mouseData)==0)
lor = log(fitPA(mouseData,cl=pData(mouseData)[,3])$oddsRatio)
plotBubble(lor,sparsity,main="lor ~ sparsity")
# Example 2
x = runif(100000)
y = runif(100000)
plotBubble(y,x)

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.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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(metagenomeSeq)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5

Loading required package: RColorBrewer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/metagenomeSeq/plotBubble.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotBubble
> ### Title: Basic plot of binned vectors.
> ### Aliases: plotBubble
> 
> ### ** Examples
> 
> 
> data(mouseData)
> mouseData = mouseData[which(rowSums(mouseData)>139),]
> sparsity = rowMeans(MRcounts(mouseData)==0)
> lor = log(fitPA(mouseData,cl=pData(mouseData)[,3])$oddsRatio)
> plotBubble(lor,sparsity,main="lor ~ sparsity")
> # Example 2
> x = runif(100000)
> y = runif(100000)
> plotBubble(y,x)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>