Error in creating PCOA plot

[Almas Gheyas]

Hi, 

I am trying to run PCA and PCOA analyses and create the plots using the to use gl.pcoa and gl.pcoa.plot functions. While I could successfully create the PCA plot, I get some error message with the PCOA plot. I am using "dev" version of DartRverse. 

Here is what I have tried: 

# PCA (without specifying any genetic distance matrix)

pcoa <- gl.pcoa(gl_flt)  

gl.pcoa.plot(pcoa, gl_flt)    # creating PCA plot

The above command successfully created PCA plot showing the individuals and population names. 

# PCOA (with nei's genetic distance)

dnei <- gl.dist.pop(gl_flt, method="nei")

pcoa2 <- gl.pcoa(dnei)

gl.pcoa.plot(pcoa2, gl_flt) 

Starting gl.pcoa.plot Processing an ordination file (glPca) Processing genlight object with SNP data Error in data.frame(..., check.names = FALSE) :  

arguments imply differing number of rows: 9, 266  

Any suggestions what might be the problem here? 

gl.compliance.check(gl_flt)  shows "population assignment confirmed".

So this cannot be the issue as was described as a potential cause in a previous conversation. 

Thank you!

Almas

[Jose Luis Mijangos]

Hi Almas,

Based on the genlight object and the code that you shared with me, I found that the problem is that you are calculating the distance between two populations, PCA requires at least three pairwise distances, i.e. at least three populations.

Cheers,

Luis 

[Almas Gheyas]

HI Luis, 

Thanks for this but I its only in the subset of the samples that I shared  with you has only two populations. In my original larger set, there are 8-9 populations. 

I will send you a larger subset with 3-4 populations. 

cheers

Almas