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enblacar / SCpubr

Generate high quality, publication ready visualizations for single cell transcriptomics data.
https://enblacar.github.io/SCpubr-book/
GNU General Public License v3.0
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Fix typo | do_ViolinPlot | Spelling Error #67

Closed maximelepetit closed 3 months ago

maximelepetit commented 3 months ago

Hi , Thanks a lot for developing this great visualization package !

Bug:

There's a spelling mistake regarding the error message in the do_ViolinPlot function with the split.by parameter, when keeping the boxplots.
The error message is : ✖ Boxplots are not implemented when split.by is set. Set plot_boxplots = FALSE.NA

According to manual of do_ViolinPlot the true parameter name is : plot_boxplot (without the "s") .

Reproducible example:

SCpubr::do_ViolinPlot(
  sample = parse_melano_invivo,
  features = markers_trt.top10.pct$gene,
  split.by   = "condition",
  flip = T
)

SCpubr version:

2.0.2

Session info:

> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] lemon_0.4.9          GSEABase_1.60.0      graph_1.76.0         annotate_1.76.0     
 [5] XML_3.99-0.16.1      AnnotationDbi_1.60.2 IRanges_2.32.0       S4Vectors_0.36.2    
 [9] Biobase_2.58.0       BiocGenerics_0.44.0  AUCell_1.20.2        readxl_1.4.3        
[13] clustree_0.5.1       ggraph_2.1.0         cluster_2.1.6        SCpubr_2.0.2        
[17] gridExtra_2.3        hdf5r_1.3.9          hrbrthemes_0.8.0     patchwork_1.2.0     
[21] glmGamPoi_1.10.2     Seurat_5.0.1         SeuratObject_5.0.1   sp_2.1-3            
[25] lubridate_1.9.3      forcats_1.0.0        stringr_1.5.1        dplyr_1.1.4         
[29] purrr_1.0.2          readr_2.1.5          tidyr_1.3.1          tibble_3.2.1        
[33] ggplot2_3.5.0        tidyverse_2.0.0     

loaded via a namespace (and not attached):
  [1] utf8_1.2.4                  R.utils_2.12.3              spatstat.explore_3.2-6     
  [4] reticulate_1.35.0           tidyselect_1.2.0            RSQLite_2.3.5              
  [7] htmlwidgets_1.6.4           grid_4.2.3                  Rtsne_0.17                 
 [10] munsell_0.5.0               codetools_0.2-19            ica_1.0-3                  
 [13] future_1.33.1               miniUI_0.1.1.1              withr_3.0.0                
 [16] spatstat.random_3.2-2       colorspace_2.1-0            progressr_0.14.0           
 [19] knitr_1.45                  rstudioapi_0.15.0           ROCR_1.0-11                
 [22] tensor_1.5                  Rttf2pt1_1.3.12             fontLiberation_0.1.0       
 [25] listenv_0.9.1               labeling_0.4.3              MatrixGenerics_1.10.0      
 [28] GenomeInfoDbData_1.2.9      polyclip_1.10-6             farver_2.1.1               
 [31] bit64_4.0.5                 parallelly_1.37.0           vctrs_0.6.5                
 [34] generics_0.1.3              xfun_0.42                   timechange_0.3.0           
 [37] fontquiver_0.2.1            R6_2.5.1                    GenomeInfoDb_1.34.9        
 [40] graphlayouts_1.1.0          gridGraphics_0.5-1          cachem_1.0.8               
 [43] bitops_1.0-7                spatstat.utils_3.0-4        DelayedArray_0.24.0        
 [46] assertthat_0.2.1            promises_1.2.1              scales_1.3.0               
 [49] gtable_0.3.4                globals_0.16.2              goftest_1.2-3              
 [52] spam_2.10-0                 tidygraph_1.2.2             rlang_1.1.3                
 [55] systemfonts_1.0.5           splines_4.2.3               extrafontdb_1.0            
 [58] lazyeval_0.2.2              spatstat.geom_3.2-8         BiocManager_1.30.22        
 [61] yaml_2.3.8                  reshape2_1.4.4              abind_1.4-5                
 [64] httpuv_1.6.14               extrafont_0.19              tools_4.2.3                
 [67] ggplotify_0.1.2             ellipsis_0.3.2              RColorBrewer_1.1-3         
 [70] ggridges_0.5.6              Rcpp_1.0.12                 plyr_1.8.9                 
 [73] sparseMatrixStats_1.10.0    zlibbioc_1.44.0             RCurl_1.98-1.14            
 [76] deldir_2.0-2                viridis_0.6.5               pbapply_1.7-2              
 [79] cowplot_1.1.3               zoo_1.8-12                  SummarizedExperiment_1.28.0
 [82] ggrepel_0.9.5               fs_1.6.3                    crul_1.4.0                 
 [85] magrittr_2.0.3              data.table_1.15.0           RSpectra_0.16-1            
 [88] scattermore_1.2             lmtest_0.9-40               RANN_2.6.1                 
 [91] fitdistrplus_1.1-11         matrixStats_1.1.0           hms_1.1.3                  
 [94] mime_0.12                   evaluate_0.23               xtable_1.8-4               
 [97] fastDummies_1.7.3           compiler_4.2.3              fontBitstreamVera_0.1.1    
[100] KernSmooth_2.23-22          crayon_1.5.2                R.oo_1.26.0                
[103] htmltools_0.5.7             later_1.3.2                 tzdb_0.4.0                 
[106] DBI_1.2.2                   tweenr_2.0.3                MASS_7.3-60.0.1            
[109] Matrix_1.6-5                cli_3.6.2                   R.methodsS3_1.8.2          
[112] parallel_4.2.3              dotCall64_1.1-1             igraph_1.3.5               
[115] GenomicRanges_1.50.2        pkgconfig_2.0.3             plotly_4.10.4              
[118] spatstat.sparse_3.0-3       XVector_0.38.0              yulab.utils_0.1.4          
[121] digest_0.6.34               sctransform_0.4.1           RcppAnnoy_0.0.22           
[124] Biostrings_2.66.0           httpcode_0.3.0              spatstat.data_3.0-4        
[127] cellranger_1.1.0            rmarkdown_2.25              leiden_0.4.3.1             
[130] uwot_0.1.16                 DelayedMatrixStats_1.20.0   gdtools_0.3.6              
[133] curl_5.2.0                  shiny_1.8.0                 lifecycle_1.0.4            
[136] nlme_3.1-164                jsonlite_1.8.8              viridisLite_0.4.2          
[139] fansi_1.0.6                 pillar_1.9.0                lattice_0.22-5             
[142] KEGGREST_1.38.0             fastmap_1.1.1               httr_1.4.7                 
[145] survival_3.5-8              glue_1.7.0                  png_0.1-8                  
[148] bit_4.0.5                   presto_1.0.0                ggforce_0.4.2              
[151] stringi_1.8.3               blob_1.2.4                  gfonts_0.2.0               
[154] RcppHNSW_0.6.0              memoise_2.0.1               renv_1.0.7                 
[157] irlba_2.3.5.1               future.apply_1.11.1
enblacar commented 3 months ago

Hi @maximelepetit,

Thank you for using my package and taking the time to report this! I have fixed the typo and will roll out on the next update!

Best, Enrique