3D PCOA plotting

[jlsr]

Hello everyone,

I ran my data for PCoA and was able to generate a 2D diagram. I tried plotting it in 3d using the script gl.pcoa.plot.3d(pcoa, g, xaxis = 1, yaxis = 2, zaxis = 3), however, no diagram appeared. The following notes were on the console after running the line:

Starting gl.pcoa.plot.3d 

  Extracting coordinates of PCoA solution

  Plotting three specified axes

[1] 1.593161 1.259051 1.035970

Completed: gl.pcoa.plot.3d 

NULL

Is there any problem with my data?

Thank you very much.

Laurence

[Bernd.Gruber]

Hi Laurence,

 

Sounds like there was a plot created following the output you stated.

 

So can you check if there is an additional window that popped up?

 

Also which system you are using?  As for the 3d plot to work you need quartz installed on Macs and rgl binaries installed on Linux. On Windows it should work out of the box (but an additional window will pop up).

Cheers, Bernd

 

 

 

 

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[jlsr]

Hello Dr. Bernd,

There's no pop-up window after the line was executed. Also, I already installed quartz. 

Thank you for answering my question.

Laurence

[jlsr]

Good day Dr. Bernd,

I was able to generate 3D PCoA. I forgot to restart the R and my computer after installing Quartz. I think that solved the issue. I have another concern regarding 3D PCoA. I am planning to incorporate the locations where my samples were collected and I was wondering if each location can be represented by a specific color in the 3D plot. I am not sure how to add the locations' row/column in the SNP and silico-DArT csv file and are there any additional script when constructing 3D PCoA with different colors.

This is the script I used for the PCoA:

pc <- gl.pcoa(i, nfactors = 5)

gl.pcoa.plot.3d(pc,i, title= "PCA", 

                xaxis=1, 

                yaxis=2, 

                zaxis=3,  

                shape="sphere", 

                radius=2, 

                legend="topright", 

                verbose=NULL)

Thank you very much.

Laurence

[Bernd.Gruber]

Hi Laurence,

 

the 3d pcoa uses the population definition to do the 3d plot.

 

So you would need to redefine your population definition of your genlight object (called “I” in your example)

 

 

So something like

 

pop(i) <- factor that codes for each individual location.

 

 

Another way is to have the factor included in your metadata when you load your data (assuming it is dart data) via

 

gl.read.dart(“dartfile”, “metadatafile“)

 

you would need to add a column maybe called “location” to your metadata file that codes for the color of the individuals.

 

And then you could do:

 

 

pop(i) <- i@other$ind.metrics$location

 

 

And the final more hacking version is to have a look at the gl.pcoa.plot.3d function. There you can see that the function is mostly a wrapper around functions from the pca3d package. As you can see there, the plot command is at the end here:

 

 

   pca3d::pca3d(coords, shape = shape, radius = radius,

            group = row.names(glPca$scores), legend = legend,

            axe.titles = c(xlab, ylab, zlab))

 

 

and groupings are defined via the group argument.

 

Finally I just found an cool looking new github package that uses shaders to create 3d ggplot in case you want to dig down even deeper.

 

https://www.tylermw.com/3d-ggplots-with-rayshader/

 

 

Might be an addtion to the next version…

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[jlsr]

Thank you Dr. Bernd! I will try this.

Laurence