diffFactors {chroGPS} | R Documentation

## Performs differential analysis of chroGPS-factors maps based on Procrustes analysis.

### Description

The function uses Procrustes analysis to compare two chroGPS-factors MDS solutions, providing a visual map highlighting differences and a ranked list of Procrustes squared errors between analog replicated factors in both maps.

### Usage

    diffFactors(m1,m2,name1='mds1',name2='mds2',minPoints=10,poslegend='topleft',plot=TRUE,pointcol.m1='red',pointcol.m2='green',textcol.m1='black',textcol.m2='grey',pch.m1=19,pch.m2=19,cex.m1=1,cex.m2=1,segcol='blue',...)

### Arguments

`m1` | A `mds` object, containing a chroGPS-factors MDS map.
`m2` | A `mds` object, containing a chroGPS-factors MDS map, must be conformable with m1 (same number of elements and in the same order in the MDS points).
`name1` | Name for m1, by default 'mds1'
`name2` | Name for m2, by default 'mds2'
`minPoints` | Minimum number of points in each of the MDS objects.
`poslegend` | Position for the map legend, passed on to `legend` function.
`plot` | Wether to plot the differential map or not (in case we only want to retrieve Procrustes errors).
`pointcol.m1` | Color vector for points in MDS1.
`pointcol.m2` | Color vector for points in MDS2.
`textcol.m1` | Color vector for labels in MDS1. Labels are taken from MDS points rownames.
`textcol.m2` | Color vector for labels in MDS2. Labels are taken from MDS points rownames.
`pch.m1` | Pch for MDS1 points.
`pch.m2` | Pch for MDS2 points.
`cex.m1` | Cex for MDS1 points.
`cex.m2` | Cex for MDS2 points.
`segcol` | Color for segments joining replicates from both MDS.
`...` | Further arguments passed on to the `plot` function.

### Value

The function returns a data frame with Procrustes errors between paired replicates in both chroGPS-factors MDS maps.

### Author(s)

Oscar Reina.

### See Also

See functions `distGPS, mds` for generating chroGPS-factors maps.

### Examples

    ## Not run

    data(s2)
    data(repliSeq)
    library(gplots)

    # Modify colors and add some transparency
    fnames <- s2names$Factor
    s2names$Color[s2names$Color=='grey'] <- 'orange'
    fcolors <- paste(col2hex(s2names$Color),'BB',sep='')
    bcolors <- paste(col2hex(s2names$Color),'FF',sep='')

    # Select time points to compare
    m1 <- m.origs[['Early.Mid']]
    m2 <- m.origs[['Late']]

    ## Perform differential Procrustes analysis
    pp <- diffFactors(m1,m2)

    ## Plot both maps before and after adjustment
    m3 <- pp$mds3
    plot(0,xlim=c(-1,1),ylim=c(-1,1),xlab='',ylab='',xaxt='n',yaxt='n',col='NA')
    segments(m1@points[,1],m1@points[,2],m3@points[,1],m3@points[,2],col='red')
    par(new=TRUE)
    plot(m1,drawlabels=TRUE,labels=s2names$Factor,point.pch=19,point.cex=4,text.cex=0.75,point.col=s2names$Color,main=sprintf('S2@Origins, adjusted (Avgdist-isoMDS)'),font=2,xlim=c(-1,1),ylim=c(-1,1))
    par(new=TRUE)
    plot(m3,drawlabels=TRUE,labels=s2names$Factor,point.pch=19,point.cex=4,text.cex=0.75,point.col=s2names$Darkcolor,text.col='grey',main='',xaxt='n',yaxt='n',font=2,xlim=c(-1,1),ylim=c(-1,1))

    ## Plot Procrustes errors
    pp <- pp$procrustes
    par(las=1,mar=c(4,12,4,4)); barplot(sort(residuals(pp),decr=TRUE),horiz=TRUE,xlim=c(0,max(residuals(pp))+.1),col=heat.colors(length(residuals(pp))),main='Procrustes errors')
    hist(residuals(pp),breaks=50)

[Package chroGPS version 2.4.0 Index]