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SNPRelate; Plot looking blank

I am doing PCA analysis through SNPRelate. Its Generating the PCA plot but completely blank without any error. What to do?

Other question is that how can I add population information in my .gds file as I am working on a plant species. SNPRelate tutorial example file is working very smoothly but I its not user friendly for others.

snprelate
• 3,905 views • link
updated by Ram Ram • written by kumar.vinod81 kumar.vinod81

Can you post the piece of code that you are using ?

• 1 views • link
written by GouthamAtla GouthamAtla 
> # make a data.frame
> tab <- data.frame(sample.id = pca$sample.id,
+ EV1 = pca$eigenvect[,1], # the first eigenvector
+ EV2 = pca$eigenvect[,2], # the second eigenvector
+ stringsAsFactors = FALSE)
> head(tab)
  sample.id         EV1         EV2
1   NA19152  0.08411287  0.01226860
2   NA19139  0.08360644  0.01085849
3   NA18912  0.08110808  0.01184524
4   NA19160  0.08680864  0.01447106
5   NA07034 -0.03109761 -0.07709255
6   NA07055 -0.03228450 -0.08155730
> # draw
> plot(tab$EV2, tab$EV1, col=as.integer(tab$pop),
+ xlab="eigenvector 2", ylab="eigenvector 1")

Note: Results are generated from .gds file

• 0 views • link
updated by Ram Ram • written by kumar.vinod81 kumar.vinod81

One possibility could be the eigenvectors EV1 or EV2 contains NaN as values. You can check the actual value by just typing pca$eigenvect[,1] or pca$eigenvect[,2]

• 0 views • link
written by GouthamAtla GouthamAtla

but values are there in file as you look at my previous comment

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updated by Ram Ram • written by kumar.vinod81 kumar.vinod81

Then the problem is with the col=as.integer(tab$pop) as I could not see any column pop in the tab data structure.

• 1 views • link
updated by Ram Ram • written by GouthamAtla GouthamAtla

How can I add this column in my data, because in SNPRelate documentation, it is not written.

• 2 views • link
written by kumar.vinod81 kumar.vinod81

1 answer

Hi, Although this is an older post but if someone is looking for the answer, here I found one on add column to dataframe r- https://www.hdfstutorial.com/blog/add-column-to-dataframe-r/ Using this you will be able to add a new column at the place you want.

• 0 views • link
written by hdfstutorial • hdfstutorial

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