geom_boxplot with geom_jitter produces double dots

[frezza-metabolomics]

Tips for a helpful bug report:

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I found a problem with ggplot2::geom_boxplot will create a second dot of different size but identical. not all values are being replicated

Here is the code to reproduce the bug:
this is my data

 data_box_sel
         1-methylnicotinamide Conditions
CM04_026              4097964   CM4N_DKO
CM04_027              5484845   CM4N_DKO
CM04_028              4131174   CM4N_DKO
CM04_029              6466447    CM4N_WT
CM04_030              5580998    CM4N_WT
CM04_031              4524057    CM4N_WT
CM04_032              6371849   CM4N_DKO
CM04_033              5440818    CM4N_WT
CM04_034              6050115   CM4N_DKO
CM04_035              5349607    CM4N_WT
CM04_036              5361647    CM4N_WT
CM04_037              6405902   CM4N_SKO
CM04_038             13378067   CM4N_SKO
CM04_039              7068394   CM4N_SKO
CM04_040              6495043   CM4N_SKO
CM04_041              6965436    CM4N_WT
CM04_042              4719839    CM4N_WT
CM04_043              3743428    CM4N_WT
CM04_044              3424181   CM4N_SKO
CM04_045              4871067   CM4N_TKO
CM04_046              4175500   CM4N_TKO
CM04_047              4153753   CM4N_TKO
CM04_048              3797616   CM4N_TKO
CM04_049              6204417   CM4N_TKO
CM04_050              7399935   CM4N_SKO

this is the code:

     mdatBOX2 <- reshape2::melt(data_box_sel)  ## convert to long format
mdatBOX2$value <- log10(mdatBOX2$value)
    mdatBOX2 <- mdatBOX2[order(mdatBOX2$Conditions),]
#the plot
      ggplot(mdatBOX2, aes(x=factor(Conditions), y=value, fill=Conditions)) +
          geom_boxplot() +
          #viridis::scale_fill_viridis(discrete = TRUE, alpha=0.6) +
          geom_jitter(shape=5, alpha=0.7)

notice the black circular point. those should not be there.

same if I add a violin in there:

     mdatBOX2 <- reshape2::melt(data_box_sel)  ## convert to long format
mdatBOX2$value <- log10(mdatBOX2$value)
    mdatBOX2 <- mdatBOX2[order(mdatBOX2$Conditions),]
#the plot
      ggplot(mdatBOX2, aes(x=factor(Conditions), y=value, fill=Conditions)) +
      ggplot2::geom_violin(size = 0.1)+
          geom_boxplot() +
          #viridis::scale_fill_viridis(discrete = TRUE, alpha=0.6) +
          geom_jitter(shape=5, alpha=0.7)

and my session info

sessionInfo()    
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8   
[3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.utf8    

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

other attached packages:
 [1] ggfortify_0.4.16    multtest_2.54.0     Biobase_2.58.0      BiocGenerics_0.44.0
 [5] readxl_1.4.2        lubridate_1.9.2     forcats_1.0.0       stringr_1.5.0      
 [9] dplyr_1.1.2         purrr_1.0.1         readr_2.1.4         tidyr_1.3.0        
[13] tibble_3.2.1        ggplot2_3.4.2       tidyverse_2.0.0    

loaded via a namespace (and not attached):
 [1] ggrepel_0.9.3          Rcpp_1.0.10            svglite_2.1.1          lattice_0.21-8        
 [5] gtools_3.9.4           utf8_1.2.3             R6_2.5.1               cellranger_1.1.0      
 [9] plyr_1.8.8             backports_1.4.1        stats4_4.2.2           pillar_1.9.0          
[13] rlang_1.1.0            qcc_2.7                rstudioapi_0.14        car_3.1-1             
[17] EnhancedVolcano_1.16.0 hash_2.2.6.2           Matrix_1.5-3           textshaping_0.3.6     
[21] labeling_0.4.2         splines_4.2.2          munsell_0.5.0          broom_1.0.4           
[25] compiler_4.2.2         systemfonts_1.0.4      pkgconfig_2.0.3        tidyselect_1.2.0      
[29] gridExtra_2.3          viridisLite_0.4.1      fansi_1.0.4            crayon_1.5.2          
[33] tzdb_0.3.0             withr_2.5.0            ggpubr_0.6.0           MASS_7.3-58.3         
[37] grid_4.2.2             gtable_0.3.3           lifecycle_1.0.3        factoextra_1.0.7      
[41] magrittr_2.0.3         scales_1.2.1           writexl_1.4.2          cli_3.6.0             
[45] stringi_1.7.12         carData_3.0-5          inflection_1.3.6       farver_2.1.1          
[49] ggsignif_0.6.4         reshape2_1.4.4         viridis_0.6.2          ragg_1.2.5            
[53] generics_0.1.3         vctrs_0.6.0            cowplot_1.1.1          tools_4.2.2           
[57] glue_1.6.2             hms_1.1.3              abind_1.4-5            parallel_4.2.2        
[61] survival_3.4-0         timechange_0.2.0       colorspace_2.1-0       ggConvexHull_0.1.0    
[65] rstatix_0.7.2      

[teunbrand]

Does it work as intended when setting geom_boxplot(outlier.shape = NA)?

[frezza-metabolomics]

Does it work as intended when setting geom_boxplot(outlier.shape = NA)?

Thank you for your recommendation.This one solves the issue. So, in my understanding geom_boxplot() will not plot extreme outliers, and to properly plot them I will need to manually extend the yaxis to that point.

But, shouldn't this be the default state so that no artefacts being produced or give a warning?

[teunbrand]

The boxplot will draw outliers by default, unless directed otherwise. If you use the outlier.shape = NA, you don't have to extend the y-axis to include the total range of the data by default. In the development version you can use outliers = FALSE to have the default axis range fit the summarised data instead of the full data.

In any case, I think everything is working as intended here, so I'm going to close this issue.