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green-striped-gecko / dartR

Importing and Analysing DArT type snp and silicodart data
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gl.report.hwe error #662

Open jane-edgeloe opened 6 months ago

jane-edgeloe commented 6 months ago

I continue to get this same error when trying to compute HWE and Heterozygosity- see "guides_trains" error. Any help is appreciated! :)

dartR::gl.report.hwe(gl.secondaries.filtered) Starting :: Starting dartR Starting gl.report.hwe Processing genlight object with SNP data Analysing each population separately Warning: population CanalRocks [Original species: racemosa] has less than 5 individuals... skipped Registered S3 methods overwritten by 'ggtern': method from
grid.draw.ggplot ggplot2 plot.ggplot ggplot2 print.ggplot ggplot2 Error in guides_train(scales = scales$non_position_scales(), theme = theme, : could not find function "guides_train"

green-striped-gecko commented 6 months ago

This is due to the latest ggplot2 upgrade.Delete ggplot2 version 3.5 and the installdevtools::version("ggplot2", "3.4.4")That should fix it.Cheers, Bernd---------On 19 Mar 2024, at 17:44, jane-edgeloe @.***> wrote: I continue to get this same error when trying to compute HWE and Heterozygosity- see "guides_trains" error. Any help is appreciated! :)

dartR::gl.report.hwe(gl.secondaries.filtered) Starting :: Starting dartR Starting gl.report.hwe Processing genlight object with SNP data Analysing each population separately Warning: population CanalRocks [Original species: racemosa] has less than 5 individuals... skipped Registered S3 methods overwritten by 'ggtern': method from grid.draw.ggplot ggplot2 plot.ggplot ggplot2 print.ggplot ggplot2 Error in guides_train(scales = scales$non_position_scales(), theme = theme, : could not find function "guides_train"

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green-striped-gecko commented 5 months ago

That is a n error due to the new ggplot2 nbreaking some packages.You can fix that by installing the previous version.devtools::version("guide", "3.4.4")---------On 19 Mar 2024, at 17:44, jane-edgeloe @.***> wrote: I continue to get this same error when trying to compute HWE and Heterozygosity- see "guides_trains" error. Any help is appreciated! :)

dartR::gl.report.hwe(gl.secondaries.filtered) Starting :: Starting dartR Starting gl.report.hwe Processing genlight object with SNP data Analysing each population separately Warning: population CanalRocks [Original species: racemosa] has less than 5 individuals... skipped Registered S3 methods overwritten by 'ggtern': method from grid.draw.ggplot ggplot2 plot.ggplot ggplot2 print.ggplot ggplot2 Error in guides_train(scales = scales$non_position_scales(), theme = theme, : could not find function "guides_train"

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