User:Timothee Flutre/Notebook/Postdoc/2012/01/22: Difference between revisions
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ind3 1.8 2.0 | ind3 1.8 2.0 | ||
Here is the file with the commands: | Here is the file with the commands ("+0.1" is an offset which needs to be tuned with respect to the data): | ||
$ cat commands.gnuplot | $ cat commands.gnuplot | ||
set terminal postscript color | set terminal postscript color |
Revision as of 11:40, 22 January 2012
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Entry title
Assuming that the genotypes are in the IMPUTE format, we need to convert them into the EIGENSTRAT format thanks to this script: impute2eigenstrat.py -i genotypes_allchrs.impute.gz -o mystudy -l MyStudy Now we can run the PCA: smartpca.perl -i mystudy_eigenstrat_genotypes.txt -a mystudy_eigenstrat_snp.txt -b mystudy_eigenstrat_indiv.txt \ -o mystudy_eigenstrat_pca.txt -p mystudy_eigenstrat_plot -e mystudy_eigenstrat_eigenvalues.txt -l mystudy_eigenstrat_log.txt -s 6.0
As an example, let's assume that the output data file from EIGENSOFT containing the PCs is like this (3 individuals, 2 PCs): $ cat data.txt ind1 2.0 2.0 ind2 2.5 1.8 ind3 1.8 2.0 Here is the file with the commands ("+0.1" is an offset which needs to be tuned with respect to the data): $ cat commands.gnuplot set terminal postscript color set title "" set xlabel "eigenvector 1" set ylabel "eigenvector 2" #plot "mystudy_eigenstrat_pca.txt.evec" using 2:3 title "MyStudy" plot "data.txt" using 2:3 title "Data", "" using 2:($3+0.1):1 with labels notitle ## pause 9999 We can obtain the new plot like this: $ gnuplot < commands.gnuplot > newplot.ps; ps2pdf newplot.ps newplot.pdf |