Generating an MDS plot in R for population stratification
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13 months ago
nliberman • 0

Hello,

I'm very new to bioinformatics and I'm just starting out using PLINK and R to perform a GWAS for the first time. I've generated a .mds file through PLINK of 10 dimensions that looks like this file:

With many more rows of course. I'm trying to graph an MDS plot of this data but I'm not sure how? I found this code online:

m <- read.table('pca.mds', header = TRUE)
m <- as.matrix(m[, 4:13])
mds <- cmdscale(as.dist(1-m))
plot(mds)

But this generates the error:

non-square matrixnumber of items to replace is not a 
multiple of replacement length
Error in dimnames(points) <- list(rn, NULL) : 
length of 'dimnames' [1] not equal to array extent

Can someone help explain why this is happening and how to fix it? I'm very new to this, and I'd like to generate a plot that looks like:

sample mds plot

Probably with more dimensions though obviously. Or I'm not really sure if there's a better way to generate an MDS plot for the purposes of population stratification? Any help would be much appreciated!

R MDS Stratification PCA PLINK • 726 views
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Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.

code_formatting

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Thank you for the tip! Fixed :)

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Thank you for bettering your post!

There was one step that needed to be done a little differently: the gist link must be pasted directly in the text and not using the Hyperlink option on the toolbar. Doing it the former way embeds the gist in the post.

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