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popgenmethods / smcpp

SMC++ infers population history from whole-genome sequence data.
GNU General Public License v3.0
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question about commond cv and plot #121

Open willright28 opened 5 years ago

willright28 commented 5 years ago

Hi dear @terhorst : When I tried to use one of cv's parameter spline to plot smooth splines, and found out that all of the three optiions cubic,pchip,piecewisedid not work for me unfortunately, all I got is cubic-like or piecewise-like spline. So could you please kindly guide me how to draw smooth splines, or if I misunderstood the spline's usage please correct me. Thanks in advance!

terhorst commented 5 years ago

Could you post the command line you used as well as whatever output (PDF) it generated?

willright28 commented 5 years ago

Sure，such as when I used this cv commond : time smc++ cv -o /gpfs/home/chenyl/biodata/test_seq/LS003/LS003_HF \ --timepoints 1e1 1e6 \ --thinning 3000 \ --ftol 0.01 \ --Nmax 1e9 --Nmin 0 \ --regularization-penalty 5 \ **--spline cubic \** --folds 5 \ 4.6e-9 /gpfs/home/chenyl/biodata/test_seq/LS003/LS003_HF/chr*.smc.gz && echo "done" and this plot commond: smc++ plot -c plot_LS003.pdf /gpfs/home/chenyl/biodata/test_seq/LS003/LS003_HF/model.final.json -g 5.5 -x 1e1 1e6 -y 0 1e6 I got this output: plot_LS003_year.pdf and also this cv commond with the default plot commond as i mention above, time smc++ cv -o /gpfs/home/chenyl/biodata/test_seq/LS004/LS004_rawdata \ --timepoints 1e1 1e6 \ --thinning 3000 \ --ftol 0.01 \ --Nmax 1e9 --Nmin 0 \ --regularization-penalty 5 \ **--spline pchip \** --folds 5 \ 4.6e-9 /gpfs/home/chenyl/biodata/test_seq/LS004/LS004_rawdata/chr*.smc.gz && echo "done" I got this output: plot_LS004.pdf And the --spline piecewise worked as the same.

Thanks for helping!