plotPcs: Plot many side by side scores XOR loadings plots

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/pca.R

Description

A function that can be used to visualise many PCs plotted against each other

Usage

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plotPcs(object, pcs = 1:nP(object), type = c("scores", "loadings"),
  sl = NULL, hotelling = 0.95, ...)

Arguments

object

pcaRes a pcaRes object

pcs

numeric which pcs to plot

type

character Either "scores" or "loadings" for scores or loadings plot respectively

sl

character Text labels to plot instead of a point, if NULL points are plotted instead of text

hotelling

numeric Significance level for the confidence ellipse. NULL means that no ellipse is drawn.

...

Further arguments to pairs on which this function is based.

Details

Uses pairs to provide side-by-side plots. Note that this function only plots scores or loadings but not both in the same plot.

Value

None, used for side effect.

Author(s)

Henning Redestig

See Also

prcomp, pca, princomp, slplot

Examples

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data(iris)
pcIr <- pca(iris[,1:4], nPcs=3,  method="svd")
plotPcs(pcIr, col=as.integer(iris[,4]) + 1)

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

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

pcaMethods documentation built on Nov. 1, 2018, 2:45 a.m.