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millanek / fineRADstructure

A package for population structure inference from RAD-seq data
https://www.milan-malinsky.org/fineradstructure
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Help plotting #17

Open Dieggarp opened 3 years ago

Dieggarp commented 3 years ago

Hi all,

I'm a new user of R and need some help to correctly plot my finestructure. I'm trying to reorder the position of my different individuals in the plots and even though I am able to get plots, I don't know what to change in the script to do that.

Is there a file or line in the script I would need to change in order for the plot to have the order of populations I want to?

I attached the file I want to change. I need the group in the center with the highest co-ancestry levels to be on the bottom left side of the plot.

image

Thanks! Diego

Yyeserin commented 1 year ago

Hi Dieogo,

Have you figured it out?

As I understand, the population names should also have a specific format. This website says they shouldn't have any numbers: https://thierrygosselin.github.io/radiator/reference/write_fineradstructure.html

But the fineRADstructurePlot.rmd says:

"## NOTE: if your population labels don't correspond to the format we used (NAME) YOU MAY HAVE TROUBLE HERE. YOU MAY NEED TO RENAME THEM INTO THIS FORM AND DEFINE YOUR POPULATION NAMES IN popnamesplot BELOW.

I don't understand what "NAME" this means. Like "SPA<1>"?

R code anyway extracts population names from the sample names in a strange way. According to the R code it does it "IN A REVERSIBLE FORMAT (I.E LOSSLESS)". But I don't get what this means.

I will be very glad if you could kindly explain how you managed to order the populations.

Many thanks.

Best regards, Yeserin.