Last data update: 2014.03.03

 R: Biplot of component analysis
biplotResR Documentation

Biplot of component analysis

Description

Generate a biplot of component analysis results

Usage

biplotRes(object, type, comps, block, title=NULL, colorCol=NULL,
                 sizeValues=c(2, 4), shapeValues=c(17, 0), background=TRUE,
                 pointSize=4, labelSize=NULL, axisSize=NULL, titleSize=NULL)

Arguments

object

caClass object containing component analysis results

type

Character specifying which components to plot; "common", "individual" or "both"

comps

Components to plot. If combined=FALSE, specifies the component indices to use as x and y for the plot. Otherwise, the component from the first block and the component from second block to plot together.

block

Which block to plot, either "1" or "2" or the name of the block.

title

Plot title

colorCol

Character specifying a pData column to use to colorise the plot points

sizeValues

Vector containing sizes for scores and loadings

shapeValues

Vector indicating the shapes for scores and loadings

background

Logical, whether to use a grey background

pointSize

Size of plot points

labelSize

Size of plot labels if not NULL

axisSize

Size of axis text

titleSize

Size of title text

Value

ggplot2 object

Author(s)

Patricia Sebastian-Leon

Examples

data("STATegRa_S3")
B1 <- createOmicsExpressionSet(Data=Block1.PCA,pData=ed.PCA,
                               pDataDescr=c("classname"))
B2 <- createOmicsExpressionSet(Data=Block2.PCA,
                               pData=ed.PCA,pDataDescr=c("classname"))
# Omics components analysis
discoRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
                              method="DISCOSCA",Rcommon=2,Rspecific=c(2,2),
                              center=TRUE,scale=TRUE,weight=TRUE)
jiveRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
                             method="JIVE",Rcommon=2,Rspecific=c(2,2),
                             center=TRUE,scale=TRUE,weight=TRUE)

o2plsRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
                              method="O2PLS",Rcommon=2,Rspecific=c(2,2),
                              center=TRUE,scale=TRUE,weight=TRUE)

# Biplot common part. DISCO-SCA

biplotRes(object=discoRes,type="common",comps=c(1,2),block="",
          title=NULL,colorCol="classname",sizeValues=c(2,4),
          shapeValues=c(17,0),background=TRUE,pointSize=4,
          labelSize=NULL,axisSize=NULL,titleSize=NULL)

# Biplot common part. O2PLS

p1 <- biplotRes(object=o2plsRes,type="common",comps=c(1,2),
                block="expr",title=NULL,colorCol="classname",
                sizeValues=c(2,4),shapeValues=c(17,0),
                background=TRUE,pointSize=4,labelSize=NULL,
                axisSize=NULL,titleSize=NULL)
p2 <- biplotRes(object=o2plsRes,type="common",comps=c(1,2),
                block="mirna",title=NULL,colorCol="classname",
                sizeValues=c(2,4),shapeValues=c(17,0),
                background=TRUE,pointSize=4,labelSize=NULL,
                axisSize=NULL,titleSize=NULL)

# Biplot distinctive part. O2PLS

p1 <- biplotRes(object=discoRes,type="individual",comps=c(1,2),
                block="expr",title=NULL,colorCol="classname",
                sizeValues=c(2,4),shapeValues=c(17,0),
                background=TRUE,pointSize=4,labelSize=NULL,
                axisSize=NULL,titleSize=NULL)
p2 <- biplotRes(object=discoRes,type="individual",comps=c(1,2),
                block="mirna",title=NULL,colorCol="classname",
                sizeValues=c(2,4),shapeValues=c(17,0),
                background=TRUE,pointSize=4,labelSize=NULL,
                axisSize=NULL,titleSize=NULL)

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(STATegRa)
Warning message:
replacing previous import 'Biobase::combine' by 'gridExtra::combine' when loading 'STATegRa' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/STATegRa/biplotRes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: biplotRes
> ### Title: Biplot of component analysis
> ### Aliases: biplotRes biplotRes,caClass,character,numeric,character-method
> 
> ### ** Examples
> 
> data("STATegRa_S3")
> B1 <- createOmicsExpressionSet(Data=Block1.PCA,pData=ed.PCA,
+                                pDataDescr=c("classname"))
> B2 <- createOmicsExpressionSet(Data=Block2.PCA,
+                                pData=ed.PCA,pDataDescr=c("classname"))
> # Omics components analysis
> discoRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
+                               method="DISCOSCA",Rcommon=2,Rspecific=c(2,2),
+                               center=TRUE,scale=TRUE,weight=TRUE)
> jiveRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
+                              method="JIVE",Rcommon=2,Rspecific=c(2,2),
+                              center=TRUE,scale=TRUE,weight=TRUE)
> 
> o2plsRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
+                               method="O2PLS",Rcommon=2,Rspecific=c(2,2),
+                               center=TRUE,scale=TRUE,weight=TRUE)
> 
> # Biplot common part. DISCO-SCA
> 
> biplotRes(object=discoRes,type="common",comps=c(1,2),block="",
+           title=NULL,colorCol="classname",sizeValues=c(2,4),
+           shapeValues=c(17,0),background=TRUE,pointSize=4,
+           labelSize=NULL,axisSize=NULL,titleSize=NULL)
> 
> # Biplot common part. O2PLS
> 
> p1 <- biplotRes(object=o2plsRes,type="common",comps=c(1,2),
+                 block="expr",title=NULL,colorCol="classname",
+                 sizeValues=c(2,4),shapeValues=c(17,0),
+                 background=TRUE,pointSize=4,labelSize=NULL,
+                 axisSize=NULL,titleSize=NULL)
Warning message:
In data.row.names(row.names, rowsi, i) :
  some row.names duplicated: 170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338 --> row.names NOT used
> p2 <- biplotRes(object=o2plsRes,type="common",comps=c(1,2),
+                 block="mirna",title=NULL,colorCol="classname",
+                 sizeValues=c(2,4),shapeValues=c(17,0),
+                 background=TRUE,pointSize=4,labelSize=NULL,
+                 axisSize=NULL,titleSize=NULL)
Warning message:
In data.row.names(row.names, rowsi, i) :
  some row.names duplicated: 170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338 --> row.names NOT used
> 
> # Biplot distinctive part. O2PLS
> 
> p1 <- biplotRes(object=discoRes,type="individual",comps=c(1,2),
+                 block="expr",title=NULL,colorCol="classname",
+                 sizeValues=c(2,4),shapeValues=c(17,0),
+                 background=TRUE,pointSize=4,labelSize=NULL,
+                 axisSize=NULL,titleSize=NULL)
Warning message:
In data.row.names(row.names, rowsi, i) :
  some row.names duplicated: 170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338 --> row.names NOT used
> p2 <- biplotRes(object=discoRes,type="individual",comps=c(1,2),
+                 block="mirna",title=NULL,colorCol="classname",
+                 sizeValues=c(2,4),shapeValues=c(17,0),
+                 background=TRUE,pointSize=4,labelSize=NULL,
+                 axisSize=NULL,titleSize=NULL)
Warning message:
In data.row.names(row.names, rowsi, i) :
  some row.names duplicated: 170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338 --> row.names NOT used
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO