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TiagoOlivoto / metan

Package for multi-environment trial analysis
https://tiagoolivoto.github.io/metan/
GNU General Public License v3.0
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Problem with plot.gge or plot function #22

Closed shahbazahmed108 closed 1 year ago

shahbazahmed108 commented 1 year ago

Hello, thank you for developing such a great package, I'm running into a problem in the plot function when I run it on the output of gge() function. The issue is lines pointing to the individual genotypes in the graph, I have more than 100 lines, and when I try to plot them, those lines make the figure very messy, the issue was solved in plot_scores for ammi analysis by using the command repel= FALSE but there is no such option in plot() command. Could you please help me with that? I have attached the figure. I have tried changing font size and shape size, but couldn't make these lines go away Thank you

shahbazahmed108 commented 1 year ago

I kinda figure out the solution by restarting the R and not running ggrepel library, GitHub won't let me delete the issue

TiagoOlivoto commented 1 year ago

Hi, @shahbazahmed108 I just included an argument repel in plot.gge(), which should work similar than plot_scores(). Install the dev version of metan from gitthub and see if it works. 

library(metan)
#> Registered S3 method overwritten by 'GGally':
#>   method from   
#>   +.gg   ggplot2
#> |=========================================================|
#> | Multi-Environment Trial Analysis (metan) v1.17.0        |
#> | Author: Tiago Olivoto                                   |
#> | Type 'citation('metan')' to know how to cite metan      |
#> | Type 'vignette('metan_start')' for a short tutorial     |
#> | Visit 'https://bit.ly/pkgmetan' for a complete tutorial |
#> |=========================================================|
mod <- gge(data_ge, ENV, GEN, GY)
plot(mod, repel = TRUE) # DEFAULT

plot(mod, repel = FALSE)

Created on 2023-02-14 with reprex v2.0.2

Since this is not a bug, I'm closing this now. Feel free to write if you have any questions. Best regards