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Last data update: 2014.03.03

R: Plot a overlaid scores and loadings plot

biplot-methods

R Documentation

Plot a overlaid scores and loadings plot

Description

Visualize two-components simultaneously

Usage

## S3 method for class 'pcaRes'
biplot(x, choices = 1:2, scale = 1, pc.biplot = FALSE,
  ...)

## S4 method for signature 'pcaRes'
biplot(x, choices = 1:2, scale = 1, pc.biplot = FALSE,
  ...)

Arguments

`x`	a pcaRes object
`choices`	which two pcs to plot
`scale`	The variables are scaled by lambda^scale and the observations are scaled by lambda ^ (1-scale) where `lambda` are the singular values as computed by `princomp`. Normally 0 <= scale <= 1, and a warning will be issued if the specified 'scale' is outside this range.
`pc.biplot`	If true, use what Gabriel (1971) refers to as a "principal component biplot", with lambda = 1 and observations scaled up by sqrt(n) and variables scaled down by sqrt(n). Then the inner products between variables approximate covariances and distances between observations approximate Mahalanobis distance.
`...`	optional arguments to be passed to `biplot.default`.

Details

This is a method for the generic function 'biplot'. There is considerable confusion over the precise definitions: those of the original paper, Gabriel (1971), are followed here. Gabriel and Odoroff (1990) use the same definitions, but their plots actually correspond to pc.biplot = TRUE.

Value

a plot is produced on the current graphics device.

Author(s)

Kevin Wright, Adapted from biplot.prcomp

Examples

data(iris)
pcIr <- pca(iris[,1:4])
biplot(pcIr)

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.

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(pcaMethods)
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")'.


Attaching package: 'pcaMethods'

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

    loadings

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pcaMethods/biplot-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: biplot-methods
> ### Title: Plot a overlaid scores and loadings plot
> ### Aliases: biplot,pcaRes-method biplot-methods biplot.pcaRes
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(iris)
> pcIr <- pca(iris[,1:4])
> biplot(pcIr)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>