MAPlot1 {aCGH.Spline} | R Documentation |
Produce a MA-plot showing points retained and points excluded.
MAPlot1(x, pch=46, Retcol="black", Excol="red", ylim=c(-5,5), xlim=c(0,20), xlab="log2(mean(cy5, cy3))", ylab="log2(cy5/cy3)", main="MA-plot")
x |
- ".temp" formatted data structure. |
pch |
- the point character to use defaults to 46. |
Retcol |
- the point color to use for the points retained after normalisation, defaults to "black". |
Excol |
- the point color to use for the points excluded after normalisation, defaults to "red". |
xlim |
- the x-axis limits defaults to c(0,20). |
ylim |
- the y-axis limits defaults to c(-5,5). |
xlab |
- the label for the x-axis. |
ylab |
- the label for the y-axis. |
main |
- the main title for the plot. |
Figure showing the log2(mean(red,green)) vs. the log2(red/green).
Tomas William Fitzgerald
## Set up noisy data with a bias v = seq(1,100000,0.5) d = sin(2*pi/500 * v) nd = d + rnorm(length(d),0,100) + 1000 dd = sin(2*pi/1000 * v) ndd = dd + rnorm(length(dd),0,120) + 1000 ## Create ".temp" data stucture mat = matrix(ncol=8,nrow=length(dd)) mat[,1] = log2(nd/ndd) mat[,2] = nd mat[,3] = ndd mat[,4] = 0 mat[,5] = 0 mat[,6] = 0 mat[,7] = 0 mat[,8] = 0 ## Add a few flags mat[100:150,7] = 1 ## Plot the data par(mfrow=c(2,1),mar=c(1,1,1,1)) MAPlot1(mat,ylim=c(-1,1),xlim=c(9.4,10.4))