Error ggplot?

[Ana Filipa Sobral]

Hi dartR team,

I recently installed the developing version of dartR and am now realizing I need to update  the code for a few of the functions and I am running into some errors when plotting is needed.

For example, for gl.filter.maf, I used to run:

gl.filter.maf(mtgl6, threshold = 0.01666, v = 5)

by running that now I get the following error:

Error in layer(data = data, mapping = mapping, stat = stat, geom = GeomBar,  : 
  object 'plot_colors' not found

If I run ?gl.filter.maf and follow the suggested function and respective arguments:

gl.filter.maf(mtgl6, threshold = 0.01, by.pop = FALSE, maf.limit = 0.5, pop.limit = 4,
  ind.limit = 1, recalc = FALSE, plot.out = TRUE, plot_theme = theme_dartR(),
  plot_colors_pop = discrete_palette, plot_colors_all = two_colors, bins = 25,
  save2tmp = FALSE, verbose = NULL)

I still get a similar error:

Error in layer(data = data, mapping = mapping, stat = stat, geom = GeomBoxplot,  :
  object 'two_colors' not found

What could be the problem?

Thanks!

sessionInfo()

R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 12.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
 [1] ggplotify_0.1.0    forcats_0.5.1      stringr_1.4.0      dplyr_1.0.8        purrr_0.3.4      
 [6] readr_2.1.2        tidyr_1.2.0        tibble_3.1.6       tidyverse_1.3.1    ggplotAssist_0.1.3
[11] dartR_2.4          ggplot2_3.3.5      adegenet_2.1.5     ade4_1.7-18      

loaded via a namespace (and not attached):
  [1] readxl_1.3.1        backports_1.4.1     spam_2.8-0          StAMPP_1.6.3      
  [5] plyr_1.8.6          igraph_1.2.11       sp_1.4-6            splines_4.0.4      
  [9] digest_0.6.29       yulab.utils_0.0.4   foreach_1.5.2       htmltools_0.5.2    
 [13] viridis_0.6.2       gdata_2.18.0        fansi_1.0.2         magrittr_2.0.2    
 [17] cluster_2.1.2       doParallel_1.0.17   PopGenReport_3.0.4  tzdb_0.2.0        
 [21] openxlsx_4.2.5      modelr_0.1.8        R.utils_2.11.0      colorspace_2.0-3  
 [25] rvest_1.0.2         mmod_1.3.3          haven_2.4.3         xfun_0.30          
 [29] rgdal_1.5-28        crayon_1.5.0        jsonlite_1.8.0      iterators_1.0.14  
 [33] ape_5.6-2           glue_1.6.2          gtable_0.3.0        seqinr_4.2-8      
 [37] maps_3.4.0          scales_1.1.1        mvtnorm_1.1-3       DBI_1.1.2          
 [41] GGally_2.1.2        miniUI_0.1.1.1      Rcpp_1.0.8          viridisLite_0.4.0  
 [45] xtable_1.8-4        gridGraphics_0.5-1  foreign_0.8-82      dotCall64_1.0-1    
 [49] DT_0.21             dismo_1.3-5         htmlwidgets_1.5.4   httr_1.4.2        
 [53] RColorBrewer_1.1-2  shinyAce_0.4.1      genetics_1.3.8.1.3  calibrate_1.7.7    
 [57] ellipsis_0.3.2      pkgconfig_2.0.3     reshape_0.8.8       R.methodsS3_1.8.1  
 [61] farver_2.1.0        sass_0.4.0          dbplyr_2.1.1        utf8_1.2.2        
 [65] tidyselect_1.1.2    labeling_0.4.2      rlang_1.0.2         reshape2_1.4.4    
 [69] later_1.3.0         munsell_0.5.0       cellranger_1.1.0    tools_4.0.4        
 [73] cli_3.2.0           generics_0.1.2      broom_0.7.12        fastmap_1.1.0      
 [77] knitr_1.37          fs_1.5.2            gdsfmt_1.26.1       zip_2.2.0          
 [81] RgoogleMaps_1.4.5.3 nlme_3.1-155        mime_0.12           R.oo_1.24.0        
 [85] xml2_1.3.3          gap_1.2.3-1         compiler_4.0.4      rstudioapi_0.13    
 [89] curl_4.3.2          png_0.1-7           reprex_2.0.1        bslib_0.3.1        
 [93] stringi_1.7.6       gdistance_1.3-6     fields_13.3         lattice_0.20-45    
 [97] Matrix_1.4-0        vegan_2.5-7         permute_0.9-7       vctrs_0.3.8        
[101] pillar_1.7.0        lifecycle_1.0.1     combinat_0.0-8      editData_0.1.8    
[105] jquerylib_0.1.4     data.table_1.14.2   SNPRelate_1.24.0    raster_3.5-15      
[109] httpuv_1.6.5        patchwork_1.1.1     R6_2.5.1            promises_1.2.0.1  
[113] gridExtra_2.3       rio_0.5.29          codetools_0.2-18    MASS_7.3-55        
[117] gtools_3.9.2        assertthat_0.2.1    shinyWidgets_0.6.4  withr_2.5.0        
[121] pegas_1.1           mgcv_1.8-39         parallel_4.0.4      hms_1.1.1          
[125] terra_1.5-21        grid_4.0.4          shiny_1.7.1         lubridate_1.8.0    

[Jose Luis Mijangos]

Hello Ana,

I have fixed that error. Could you please install again the dev version:

> library(dartR)

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

# Restart your R session: Menu > Session > Restart R

> library(dartR)

> gl.filter.maf(bandicoot.gl)

Cheers,

Luis

[Ana Filipa Sobral]

Hi Luis,

It worked, but now I am getting the same error when running:

gl.dist.pop(mtgl8, method = "euclidean", plot.out = TRUE,
            scale = FALSE, output = "dist", plot_theme = theme_dartR(),
            plot_colors = two_colors, save2tmp = FALSE, verbose = 5)

It seems to happen anytime plotting is needed.

However, if I run:

gl.dist.pop(mtgl8, verbose = 5)

It works.

Cheers,

Ana

[Jose Luis Mijangos]

Hi Ana,

Thank you for reporting this bug.

The issue is that the variable "two_colors", that is used to set the colors for the plot, is within the "environment" of dartR and not in the environment from which you are running the function. So, as long you don't use this variable when you call the function, it will run smoothly because the function "knows" where to find the variable. If you want to use this variable, you need to specify the environment where to find the variable (dartR's environment), for example:

res_1 <- gl.dist.pop(platypus.gl, method = "euclidean", plot.out = TRUE,
            scale = FALSE, output = "dist", plot_theme = dartR:::theme_dartR(),
            plot_colors = dartR:::two_colors, save2tmp = FALSE, verbose = 5)

# if you want to use your own colors:

res_2 <- gl.dist.pop(platypus.gl, method = "euclidean", plot.out = TRUE,
                     scale = FALSE, output = "dist", plot_theme = dartR:::theme_dartR(),
                     plot_colors =c("red","blue"), save2tmp = FALSE, verbose = 5)

In the following release of dartR, we will solve this in all the functions with the same issue by adding dartR:::

Regards,

Luis

[Arthur Georges]

Hi Ana,

You can also choose colours using 

gl.select.colors(library='baseR',palette='rainbow',ncolors=12) # look at the displayed palette

mytwocolors <- gl.select.colors(library='baseR',palette='rainbow',ncolors=12,select=c(1,8)) # pick two colours

then apply them using

res_2 <- gl.dist.pop(platypus.gl, method = "euclidean", plot.out = TRUE,

                     scale = FALSE, output = "dist", plot_colors =mytwocolors, save2tmp = FALSE, verbose = 5)

Arthur

PS For shapes, try 

gl.select.shapes()

mytwoshapes <- gl.select.shapes(select=c(8,1))

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[Ana Filipa Sobral]

Hi,

Glad it was helpful.

Thank you both for your help.

Cheers,

Ana