Plot PCA figure

Description

Plot PCA figure

Usage

plotPCA(para, pcaMethod = "svdImpute", valueID = "valueNorm",
  label = "order", rmQC = TRUE, batch = FALSE, scale = "none",
  center = FALSE, saveRds = TRUE, ...)

Arguments

Value

none

Author(s)

Bo Wen wenbo@genomics.cn

Examples

para <- new("metaXpara")
pfile <- system.file("extdata/MTBLS79.txt",package = "metaX")
sfile <- system.file("extdata/MTBLS79_sampleList.txt",package = "metaX")
rawPeaks(para) <- read.delim(pfile,check.names = FALSE)
sampleListFile(para) <- sfile
para <- reSetPeaksData(para)
para <- missingValueImpute(para)
para <- transformation(para,valueID = "value")
metaX::plotPCA(para,valueID="value",scale="uv",center=TRUE)

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.

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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(metaX)
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
Loading required package: pROC
Type 'citation("pROC")' for a citation.

Attaching package: 'pROC'

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

    cov, smooth, var

Loading required package: SSPA
Loading required package: qvalue
Loading required package: lattice
Loading required package: limma

Attaching package: 'metaX'

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

    plotQC

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

    normalize, plotPCA

Warning message:
Package 'metaX' is deprecated and will be removed from Bioconductor
  version 3.3 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/metaX/plotPCA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotPCA
> ### Title: Plot PCA figure
> ### Aliases: plotPCA
> 
> ### ** Examples
> 
> para <- new("metaXpara")
> pfile <- system.file("extdata/MTBLS79.txt",package = "metaX")
> sfile <- system.file("extdata/MTBLS79_sampleList.txt",package = "metaX")
> rawPeaks(para) <- read.delim(pfile,check.names = FALSE)
> sampleListFile(para) <- sfile
> para <- reSetPeaksData(para)
> para <- missingValueImpute(para)
missingValueImpute: value
Wed Jul  6 21:54:16 2016	Missing value imputation for 'value'
Missing value in total: 3940
Missing value in QC sample: 678
Missing value in non-QC sample: 3262
Wed Jul  6 21:54:16 2016	The ratio of missing value: 4.5814%
<=0: 0
Missing value in total after missing value inputation: 0
<=0 value in total after missing value inputation: 0
> para <- transformation(para,valueID = "value")
> metaX::plotPCA(para,valueID="value",scale="uv",center=TRUE)
plot PCA for value 'value'
$fig
[1] ".//metaX-PCA.png"

$highfig
[1] ".//metaX-PCA.pdf"

$pca
svdImpute calculated PCA
Importance of component(s):
                 PC1    PC2     PC3
R2            0.2245 0.1247 0.07342
Cumulative R2 0.2245 0.3492 0.42262
500 	Variables
134 	Samples
0 	NAs ( 0 %)
3 	Calculated component(s)
Data was mean centered before running PCA 
Data was scaled before running PCA 
Scores structure:
[1] 134   3
Loadings structure:
[1] 500   3

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> dev.off()
null device 
          1 
>