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making a PCA from MASH distance result

Hello , I have to do a PCA from MASH distance results, I have created a "distances.tsv" file that have the distance results from MASH, I have to plot the dispersion of the points using R. the only tutorial that I found was this: https://replikation.github.io/bioinformatics_side/R/distanceheatmap/ but I dont need a heatmap, for comparisson porpuses, I have to do a PCA, but, how do I make a PCA from this table if the distances were already been calculated with mash dist function?

mash r pca
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written by v.berriosfarias • v.berriosfarias

1 answer

If you used the -t option in mash dist you have a square distance matrix which can be used as input for e.g. cmdscale

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written by 5heikki 5heikki

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