[adegenet-forum] DAPC scatter plot patterns

Nikki Vollmer nlv209 at hotmail.com
Thu Jul 7 19:34:57 CEST 2011

I have been using adegenet to run DAPC analyses and then plot out the results using the scatter function.  For the same dataset and parameters, when running and re-running the DAPC/scatter I get 6-7 clusters that plot out over the DAPC space in an arch pattern, however sometimes they plot in the shape of a arch like a smile, and other times in the exact same pattern except in an arch like a frown.  For publication purposes I would like all scatter plots to be arranged in the same way (I am comparing 3 different datasets) but I don't see a code in the scatter function to change how the clusters are plotted (ie. in the smile vs. frown pattern) after the fact.  I don't want to change what PCs are being plotted, just how the clusters are arranged around the axes.  Is there some code to fix this?  What I have been doing is just re-running the DAPC from the beginning and then using the scatter function over and over until I get the arch pattern that I want.  This is kinda a pain. 
If I am not being clear what my issue is I can try to provide more information.  Thanks for any help offered, I appreciate it!

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