I am using R and adegenet for ordination based genetic analysis (pca, dapc) without any problem. However, when I try to run sPCA or other spatial based analyses, all tutorials or instructions consider data files with spatial coordinates already included. I failed to find a template of a .txt or ,csv file, in order to see how to include this spatial data initially, before creating the genind object. Any advice would be highly appreciated.
Thanks!
Aristotelis
Kali nikta!
Latitude in X column and Longitude in Y column? Are you sure? I thought that X was used for longitude and Y for latitude. Please correct me if I'm wrong in this case. By the way, I realized that I was dead wrong at using crude UTM coordinates, as there was a foreign concept for a geography newbie like me, called UTM zone. My data comprises several UTM zones, which cannot be informed in my genind object. That explains why the plots looked so weird!
Aristotelis, yes! I liked your idea of subsetting the populations by region, and I'll definitely do it! I have data from different populations around the world, which I took in order to get a "global" view of how my data behaves, but surely I will take a smaller subset, focused on my area of interest (which is vast, anyway).
Thanks!
Hi Dragos!
Thank you for your reply. You mean that I have to import my genetic data and the coordinates of the individuals separately. I thought that I needed to prepare one file. I will try your suggestoin and I will tell you if this worked.
Happy new year!
Aristotelis
Hi, I'm using the same package and would like to take the opportunity to share a question that has been bugging me for a while - and I haven't found a definite answer elsewhere: Those coordenates are meant to be UTM? I've read that they're transformed/scaled prior to sPCA, but I in no tutorial they specify the coordenate system to be used -although my hunch is definitely UTM. The thing is I'm working with populations which are quite distant from each other, ranging along several UTM zones. Then, when I perform that sPCA, populations seem to cluster a lot(especially in the Y-axis), making the plot a bit ugly and up to a certain point, uninformative.
Be your ideas welcome!
Best regards and happy new year!
Dragos, hi! I tried your instructions and the introduction of the coordinates worked perfectly, thank you very much!
Guillermo, I also used WGS84, but I guess that it should work with any coordinate system. I have very distant populations too and several subpopulations within each population. I change the spatial scale in order to have meaningful results. I mean that I focus in a specific region and run the analysis within regions or populations.
Cheers
Aristotelis
Kali nikta!
Latitude in X column and Longitude in Y column? Are you sure? I thought that X was used for longitude and Y for latitude. Please correct me if I'm wrong in this case. By the way, I realized that I was dead wrong at using crude UTM coordinates, as there was a foreign concept for a geography newbie like me, called UTM zone. My data comprises several UTM zones, which cannot be informed in my genind object. That explains why the plots looked so weird!
Aristotelis, yes! I liked your idea of subsetting the populations by region, and I'll definitely do it! I have data from different populations around the world, which I took in order to get a "global" view of how my data behaves, but surely I will take a smaller subset, focused on my area of interest (which is vast, anyway).
Thanks!
Dragos, thank you very much. I will try it and I will post here the code for the whole analysis. I am also looking for a way to have geographical coordinates in the same file as the data. I will post the outcome of my tries.
Greetings
Aristotelis
I know this is an old thread, but hopefully someone will see this. First off, this thread was extremely helpful, so thank you!
Second, I imported my coordinate file and realized that the genpop object reads the populations as (1, 10, 11, 12, 14, ...., 2, 3, 4, 5) if you have more than 9 pops (less than 20 in this example). so do I order my coordinate file the same way, or do I order it in a typical (1, 2, 3, 4, 5, 6, 7 ,8, 9, 10....) format?
I can't decide which the program is going to do, and it doesn't cover this any of the supplementary material that I've read.
Thanks!
Ashley
Hello Ashley,
in similar cases I just name my populations 01, 02, 03..., 09, 10, 11, etc. I hope this will work.
Aristotelis.
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