gl.report.heterozygosity function not working

[pkri...@cesaraustralia.com]

Hi folks,

I'm fairly new to using the dartR package, but I'm having trouble obtaining a report on heterozygosity for the populations in my data.

I've tried running the gl.report.heterozygosity() function.

I'm using the latest version of RStudio, R v4.0.0, and have updated all packages. I was initially using the current CRAN version of dartR. The gl.report.heterozygosity() function would just hang and produce no output. Then I switched to the current development version of dartR - the function thenworked for a brief time, but now, for some reason which I cannot fathom it no longer works, but instead of hanging it gives the following error:

> x1 <- gl.report.heterozygosity(testset.gl, + method="pop",boxplot="standard", verbose = 5)

Starting gl.report.heterozygosity [ Build = Jacob ]

   Processing a SNP dataset

   Warning: genlight object contains monomorphic loci which will be factored into heterozygosity estimates

   Calculating Observed Heterozygosities, averaged across loci, for each population

   Calculating Expected Heterozygosities

Error in plot.new() : figure margins too large

I've tried changing plot margins [e.g. par(mar = c(0.1, 0.1, 0.1, 0.1))], but this has no effect. I also found some previous discussion on this forum about this function but this hasn't helped - I'm not sure I can install a previous version of adegenet as this apparently requires a previous version of Rtools.

Cheers,

Peter

[Bernd.Gruber]

Hi,

 

This could be an rstudio problem (the plot area is too small in your setting. Either enlarge the plot window of click on zoom to create an independent plotting window. If this does not work please let me know. The current way of plotting is not ideal (one big thing to work on is to convert to ggplot type plots as they are much easier to handle.

 

Cheers, Bernd

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[Peter Kriesner]

Thanks very much Bernd for responding so quickly. Yes, that indeed worked!

Cheers,

Peter

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