Optional graphical parameters to adjust different components of the plot
firstComponent
Integer identifying which principal component to plot on the x-axis
secondComponent
Integer identifying which principal component to plot on the x-axis
useFilenames
Boolean. If TRUE then use filenames as plot points. Otherwise just use points.
phenotype
Phenotype information
legend1pos
String indicating where to put legend for first factor
legend2pos
String indicating where to put legend for second factor
Examples
# Next 4 lines commented out to save time in package checks, and saved version used
# if (require(affydata)) {
# data(Dilution)
# eset_mmgmos <- mmgmos(Dilution)
# }
data(eset_mmgmos)
pumapca_mmgmos <- pumaPCA(eset_mmgmos)
plot(pumapca_mmgmos)
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)
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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(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/plot-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot-methods
> ### Title: Plot method for pumaPCARes objects
> ### Aliases: plot.pumaPCARes plot-methods plot,pumaPCARes-method
> ### plot,pumaPCARes,missing-method
> ### Keywords: methods hplot
>
> ### ** Examples
>
> # Next 4 lines commented out to save time in package checks, and saved version used
> # if (require(affydata)) {
> # data(Dilution)
> # eset_mmgmos <- mmgmos(Dilution)
> # }
> data(eset_mmgmos)
> pumapca_mmgmos <- pumaPCA(eset_mmgmos)
Iteration number: 1
Iteration number: 2
Iteration number: 3
Iteration number: 4
> plot(pumapca_mmgmos)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.