17. Multidimensional Scaling

Based on Dataset II, we perform a Multidimensional Scaling Anlysis.

Creates a distance matrix using the .beagle file using ngsDist:

xsbatch -c 43 --mem-per-cpu 2000 -J Dist_Corr --time 3-00 -- "ngsDist --n_threads 16 --geno ~/data/Pigeons/PBGP/PBGP--Analyses/PBGP--ANGSDRuns/PBGP--GoodSamples_WithWGSs_NoCrupestris_SNPCalling--Article--Ultra.beagle.gz --pairwise_del --seed 47 --probs --n_ind 210 --n_sites 26082 --labels ~/data/Pigeons/PBGP/PBGP--Analyses/Lists/PBGP--GoodSamples_WithWGSs_NoCrupestris--Article.labels --out ~/data/Pigeons/PBGP/PBGP--Analyses/PBGP--MDS/PBGP--GoodSamples_WithWGSs_NoCrupestris_SNPCalling--Article--Ultra.dist"

Performs MDS using get_PCA.R:

tail -n +3 ~/data/Pigeons/PBGP/PBGP--Analyses/PBGP--MDS/PBGP--GoodSamples_WithWGSs_NoCrupestris_SNPCalling--Article--Ultra.dist | Rscript --vanilla --slave $SCRIPTS/scripts/get_PCA.R --no_header --data_symm -n 10 -m "mds" -o ~/data/Pigeons/PBGP/PBGP--Analyses/PBGP--MDS/PBGP--GoodSamples_WithWGSs_NoCrupestris_SNPCalling--Article--Ultra.mds

These MDS results were plotted using the Rscript below:

• PBG--MDS.R

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