Filtering and STRUCTURE analyses
Francisco Rubianes L.
Francisco.
Bernd.Gruber
There is a gl2structure function, but since version 2.0.3 you can use the inbuilt structure functions yourself (
gl.run.structure() see examples and you need to download the non-gui version of structure for your system.
The gl.plot.structure and gl.evanno do unfortunately not work on Macs (as CLUMPP) does not run no Macs.
Finally you can using the beautiful new function.
gl.map.structure in case your samples have coordinates
from the example: ?gl.run.structure
sr <- gl.run.structure(bc, k.range = 2:5, num.k.rep = 3, exec = 'd:/programms/structure/structure.exe')
ev <- gl.evanno(sr)
qmat <- gl.plot.structure(sr, k=3, CLUMPP='d:/programms/structure/')
gl.map.structure(qmat, bc, scalex=1, scaley=0.5)
Cheers, Bernd
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Jose Luis Mijangos
Francisco Rubianes L.
Francisco Rubianes L.
very useful!!
Bernd.Gruber
You do not need to.
You can run structure from within dartR via gl.run.structure.
Or you create a csv file in structure format via
gl2structure
Cheers, Bernd
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Arthur Georges
Francisco Rubianes L.
I already installed the STRUCTURE versions. I generate my genlinght object:
gl <- gl.read.dart(filename = "YFT2.csv", ind.metafile = "meta2.csv")
my ind.metafile has_ ind ID, pop ( I have 3 areas) and lat and log. And I am using my data from dart in SNP_singlerow_ format
I am running your suggestions but when I try to run gl.run.structure , I get this error:
gl.run.structure(
+ gl,
+ exec = "C:/Users/User/Downloads/structure_windows_console/console",
+ plot.out = TRUE,
+ plot_theme = theme_dartR(),
+ save2tmp = FALSE,
+ verbose = NULL
+ )
Starting gl.run.structure
Processing genlight object with SNP data
Error in getClass(Class, where = topenv(parent.frame())) :
“gtypes” is not a defined class
any ideas why that happens?
Bernd.Gruber
On 7 Apr 2022, at 09:11, Francisco Rubianes L. <francisco...@gmail.com> wrote:
Thank you all.
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Francisco Rubianes L.
I already installed the strataG and both STRUCTURE versions but I have this error now (Sorry for bothering you!):
Starting gl.run.structure
Processing genlight object with SNP data
On Wednesday, 6 April 2022 at 18:25:51 UTC-5 Bernd. Gruber wrote:
Hi there is still a “bug” in the function. you have to install package strataG from github via
dev tools::install_github(‘ EricArcher/strataG’)
library(strataG)
and it should work.
will be fixed soon on the beta branch.
Cheers, Bernd
Thank you all.
I already installed the STRUCTURE versions. I generate my genlinght object:
gl <- gl.read.dart(filename = "YFT2.csv", ind.metafile = "meta2.csv")
my ind.metafile has_ ind ID, pop ( I have 3 areas) and lat and log. And I am using my data from dart in SNP_singlerow_ format
I am running your suggestions but when I try to run gl.run.structure , I get this error:
gl.run.structure(
+ gl,
+ exec = "C:/Users/User/Downloads/structure_windows_console/console",
+ plot.out = TRUE,
+ plot_theme = theme_dartR(),
+ save2tmp = FALSE,
+ verbose = NULL
+ )
Starting gl.run.structure
Processing genlight object with SNP data
Error in getClass(Class, where = topenv(parent.frame())) :
“gtypes” is not a defined class
any ideas why that happens?
On Tuesday, 5 April 2022 at 03:21:37 UTC-5 Arthur Georges wrote:
Or use gl.write.csv to dump your SNP scores to a simple csv file.
A
On Tuesday, April 5, 2022 at 1:02:39 PM UTC+10 francisco wrote:
Hi everyone. I have a large data base with more than 89 SNPs and I would like to filter it and produce new cvs files after filtering. Is it possible? I found the filtering tutorial but I am not sure how to create new files after filtering. Also I need to run LEA for structure analyses. I would like to know if there is a command for converting genlight objects to STRUCTURE files. My goal is to run STRUCTURE after filtering.
Any help will be greatly appreciated!Regards,
Francisco.
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Bernd.Gruber
"C:/Users/User/Downloads/structure_windows_console/console/structure.exe"
On 7 Apr 2022, at 12:37, Francisco Rubianes L. <francisco...@gmail.com> wrote:
Thank you!
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Francisco Rubianes L.
Thank you so much for your replies! The command worked, however, I have problems with the function theme_dartR. When the run finished, I obtained three graphs, however, I can't run the evanno calculations because I don't have the result from the structure run.
I ran the next code:
structure <- gl.run.structure(
gl,
k.range = 2:5,
num.k.rep=3,
exec = "C:/Users/User/Downloads/structure_windows_console/console/structure.exe",
plot.out = TRUE,
plot_theme = theme_dartR(),
save2tmp = FALSE,
verbose = NULL
)
Error in theme_dartR() : could not find function "theme_dartR"
In addition: Warning message:
Removed 3 rows containing missing values (geom_segment).
gl.evanno(gl)
Error in utils.structure.evanno(sr, plot = plot.out) :
'sr' is not a result from 'structure.run'.
Do you have any ideas on what I might be doing wrong? sorry about the insistence!
Bernd.Gruber
Can you try to leave away the theme_dartR() argument in the gl.run.structure.
This is the default anyway, hence not necessary.
You would need to define your own theme if you want to use this functionality.
And also you need to call
gl.evanno(structure)
because the output of your gl.run.structure you called ‘structure’.
Also for the gl.plot.structure you need to set it to
gl.plot.structure(structure, k=3)
Regards, Bernd
In the example I used sr as output for gl.runstructure.
From: da...@googlegroups.com <da...@googlegroups.com> On Behalf Of Francisco Rubianes L.
Sent: Saturday, 9 April 2022 5:11 PM
To: dartR <da...@googlegroups.com>
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Francisco Rubianes L.
Thank you very much for all your help! the code is working perfectly now!