R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Plot of either PCA or MDS coordinates for the distances of...

plotOrd

R Documentation

Plot of either PCA or MDS coordinates for the distances of normalized or unnormalized counts.

Description

This function plots the PCA / MDS coordinates for the "n" features of interest. Potentially uncovering batch effects or feature relationships.

Usage

plotOrd(obj, tran = TRUE, comp = 1:2, norm = TRUE, log = TRUE,
  usePCA = TRUE, useDist = FALSE, distfun = stats::dist,
  dist.method = "euclidian", n = NULL, ...)

Arguments

`obj`	A MRexperiment object or count matrix.
`tran`	Transpose the matrix.
`comp`	Which components to display
`norm`	Whether or not to normalize the counts - if MRexperiment object.
`log`	Whether or not to log2 the counts - if MRexperiment object.
`usePCA`	TRUE/FALSE whether to use PCA or MDS coordinates (TRUE is PCA).
`useDist`	TRUE/FALSE whether to calculate distances.
`distfun`	Distance function, default is stats::dist
`dist.method`	If useDist==TRUE, what method to calculate distances.
`n`	Number of features to make use of in calculating your distances.
`...`	Additional plot arguments.

Value

coordinates

Examples


data(mouseData)
cl = pData(mouseData)[,3]
plotOrd(mouseData,tran=TRUE,useDist=TRUE,pch=21,bg=factor(cl),usePCA=FALSE)

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/plotOrd.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotOrd
> ### Title: Plot of either PCA or MDS coordinates for the distances of
> ###   normalized or unnormalized counts.
> ### Aliases: plotOrd
> 
> ### ** Examples
> 
> 
> data(mouseData)
> cl = pData(mouseData)[,3]
> plotOrd(mouseData,tran=TRUE,useDist=TRUE,pch=21,bg=factor(cl),usePCA=FALSE)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>