gl.plot.structure problem / missing data?

[Nicole Mihelich]

Hello,

I have run structure on my dataset and seem to have the appropriate output, except that I get the following warning messages upon completion of gl.run.structure:

1: Removed 5 rows containing missing values (geom_segment).
2: Removed 5 rows containing missing values (geom_segment).
3: Removed 5 rows containing missing values (geom_segment).

Is this something to be concerned about? I have pretty heavily filtered my dataset, and here are the stats: 186 genotypes,  570 binary SNPs, 11.67 % missing data

I then tried to proceed with gl.plot.structure(), but I get the error message:

Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': non-numeric matrix extent

What does this error mean? Does it have something to do with missing data/the warning messages I received during gl.run.structure? How do I resolve this problem for my data? 

I tried run, plot, and map structure with the bandicoot.gl[1:100] data, and it worked fine. 

Thank you very much for your help!

Best,

Nicole

[Bernd.Gruber]

Hi Nicole,

just a guess, but it might be that your coordinates are not valid for all individuals.

you should not have missing coordinates for any individuals.

as a quick check you can use

summary(gl@other$latlon)

and there should only be lat lon’s and no NAs or coordinates such as zero etc.

you can check also via

gl.map.interactive if you get a warning using this command (it is quicker than running the structure procedure).

Cheers, Bernd

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Bernd Gruber

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Institute for Applied Ecology 

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On 30 Dec 2022, at 15:19, 'Nicole Mihelich' via dartR <da...@googlegroups.com> wrote:

Hello,

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[Jose Luis Mijangos]

Hi Nicole,

Structure truncates individual names at 11 characters. The function will fail if the names of individuals are not unique after truncation. To avoid this possible problem, a number sequence, as  shown in the code below, might be used instead of individual names.

> indNames(gl) <- as.character(1:length(indNames(gl)))

I have added this point in the function documentation and it's available in the developing version of dartR which can be installed as below:

> library(dartR)
> gl.install.vanilla.dartR(flavour = "dev")

Cheers,

Luis

[Nicole Mihelich]

Hi Luis,

Thanks so much; it is indeed working now! No errors or warnings. I greatly appreciate your help!

Best,

Nicole

[Brianna Coulter]

Hi Luis and Bernard,

I appear to be having this same issue. I've trialled renaming the individuals with a number sequence but I still get the same error when I run gl.plot.structure(). I do not have lat/longs for any of the individuals. Is this my problem?

Many thanks,

Brianna.

[Jose Luis Mijangos]

Hi Brianna,

I did not get any error using the subset of the data you sent me.

library(dartR)
bc <- gl.load("test.rds")
sr <- gl.run.structure(bc, k.range = 2:5, num.k.rep = 3, exec = './structure')
ev <- gl.evanno(sr)
qmat <- gl.plot.structure(sr, K=3)

Could you try installing the beta version of dartR, see below, and then try again running the function?

library(dartR)
gl.install.vanilla.dartR(flavour = "dev")

Cheers,

Luis 

[Brianna Coulter]

Hi Luis,

Thanks for the suggestion. I had trialled reinstalling vanilla dartR before to no avail.

I have however solved the problem. I was running gl.run.structure() without num.k.rep but had numreps. Including num.k.rep appears to have solved this problem.

Thank you very much for your help.

Cheers,

Brianna.