plotting MDS in R with text

Question

I have a simple PLINK MDS "Cauc71.mds" :

    FID         IID     SOL     C1              C2 
1   Lezgins     lez37   0       0.0196617       0.0366344 
2   Georgians   mg47    0       0.0121934       -0.0335062 
    ...
71  Kumyk       Kumyk22 0       0.00135308      0.00216335

The following code will produce a plot in R :

d <- read.table("Cauc71.mds", header=TRUE)
plot(d$C1, d$C2, pch=20, cex=2, col = d$SOL+1)

Is there a simple way to use text-labels from the IID column {lez37, mg47 etc } instead of the pch points?

Thank you!

Welcome to SO: please format the code properly and provide a reproducible example: http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example — Mark Heckmann, Jan 14 '14 at 13:11
@Ali Yes, as a result of the comment now it is ;D (see http://stackoverflow.com/posts/21114096/revisions) — Mark Heckmann, Jan 14 '14 at 14:05
sorry for the sloppy 1st-post; very prompt and useful responses — user3193737, Jan 14 '14 at 14:45

Mark Heckmann · Answer 1 · 2014-01-14T13:50:10.210

1

You cannot define this in plot. You can only plot points, lines etc. But you could add the text afterwards, e.g.

text(d$C1, d$C2, labels=d$IID, col = d$SOL+1)

Additionally, you will probably need to position the text properly using the parameters pos or adj.

If you also want to get rid of the points, you could add the argument type="n" to the plot function.

edited Jan 14 '14 at 13:50

answered Jan 14 '14 at 13:41

Mark Heckmann

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score 0 · Answer 2 · answered Jan 14 '14 at 13:44

Try this:

d <- read.table("Cauc71.mds", header=TRUE)
plot(d$C1, d$C2, pch=20, cex=0, col = d$SOL+1)
text(d$C1, d$C2, labels=d$IID)

You can also use the ggplot2 package to generate better plots:

library(ggplot2)
ggplot(d, aes(x=C1, y=C2, label=IID))+geom_text()

enter image description here

plotting MDS in R with text

2 Answers2