gl.pcoa.plot with titles

[Iriel Joerin]

Hi!

I would like to know if there is a way to add titles for gl.PCoA plots with gl.pcoa.plot function. I couldn't find any option to do that. And maybe show the D or modify the plot in any way.

Thanks in advanced,

Iriel

[Arthur Georges]

Hi Iriel,

We wrote dartR to provide some very basic analysis and to link out to other more sophisticated packages available. As such our graphics are very rudimentary.

So with gl.pcoa.plot, if you set

plot.out

If TRUE, returns a plot object compatable with ggplot, otherwise returns a dataframe [default TRUE] the function will return a ggplot compatable object and you can play with this in ggplot2 to your heart's content. The alternative, and what I do, sadly, is export the plot as a metafile then edit and manipulate it in Adobe Illustrator. Hope this helps. A

[Iriel Joerin]

It helps. Thanks for the quick answer!

Iriel

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[Dale Maschette]

The other option which I use is if you run  gl.pcoa.plot  without the brackets it prints all the plotting code and you can just modify/add things you need. I did this so I could add unique colors etc.  

[Janice Boyd]

Dear All:

Are all these tips for someone running R ?  I am running RStudio. Executing pcoa(...) and I get  "Error in plot.new() : figure margins too large". If I first run plot.out=TRUE I don't see any plotting code.  But I can get the plot to come out if I run

> plot.out=TRUE

> pcoa <- gl.pcoa(gl.data, nfactor=5)

 

So is dartR mostly for use with R, not RStudio? 

Janice Boyd

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[Dale Maschette]

This is primarily an Rstudio issue. I just put in a pull request with a fix. In the mean time you can tell R to open the plot in a new window by putting dev.new() above your plot. eg: 

dev.new()

gl.pcoa.plot(pcoa, gl )