making a PCA from MASH distance result

Question

[v.berriosfarias]

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?

Answer 1

[5heikki]

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

[v.berriosfarias]

yes this helped, thanks so much! , now do you know a way of plotting the PCA reults without a biplot, I want my PCA plot look like this: https://cran.r-project.org/web/packages/ggfortify/vignettes/plot_pca.html