jjVolcano flip=T missing negative marker

[junyitao5462]

Greetings,

I am trying to use jjvolcano function using the PBMC sample dataset. And I intend to use flip = T to rotate the plot. However, the negative markers are missing from the figure (see attachment).

I am wondering if you can help me with this. Thank you so much for your time.

The Code are below (taken from https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html).

data('pbmc.markers')

jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('PiYG', 15)[4:12],
          size  = 3.5,
          fontface = 'italic',
          legend.position = c(0.8,0.2),
          flip = T)


> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] scRNAtoolVis_0.1.0 lubridate_1.9.3    forcats_1.0.0      stringr_1.5.1      dplyr_1.1.4        purrr_1.0.2       
 [7] readr_2.1.5        tidyr_1.3.1        tibble_3.2.1       ggplot2_3.5.1      tidyverse_2.0.0   

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3     ggdendro_0.2.0         rstudioapi_0.16.0      jsonlite_1.8.8         magrittr_2.0.3        
  [6] spatstat.utils_3.0-5   farver_2.1.2           corrplot_0.92          fs_1.6.4               vctrs_0.6.5           
 [11] ROCR_1.0-11            memoise_2.0.1          spatstat.explore_3.2-7 htmltools_0.5.8.1      usethis_2.2.3         
 [16] curl_5.2.1             sctransform_0.4.1      parallelly_1.37.1      KernSmooth_2.23-22     htmlwidgets_1.6.4     
 [21] desc_1.4.3             ica_1.0-3              plyr_1.8.9             plotly_4.10.4          zoo_1.8-12            
 [26] cachem_1.1.0           igraph_2.0.3           mime_0.12              lifecycle_1.0.4        pkgconfig_2.0.3       
 [31] Matrix_1.7-0           R6_2.5.1               fastmap_1.2.0          fitdistrplus_1.1-11    future_1.33.2         
 [36] shiny_1.8.1.1          digest_0.6.35          colorspace_2.1-0       patchwork_1.2.0        ps_1.7.6              
 [41] Seurat_5.1.0           tensor_1.5             RSpectra_0.16-1        irlba_2.3.5.1          pkgload_1.4.0         
 [46] labeling_0.4.3         progressr_0.14.0       fansi_1.0.6            spatstat.sparse_3.1-0  timechange_0.3.0      
 [51] httr_1.4.7             polyclip_1.10-6        abind_1.4-5            compiler_4.4.0         splancs_2.01-45       
 [56] remotes_2.5.0          withr_3.0.0            fastDummies_1.7.3      pkgbuild_1.4.4         R.utils_2.12.3        
 [61] MASS_7.3-60.2          sessioninfo_1.2.2      ggsci_3.2.0            tools_4.4.0            lmtest_0.9-40         
 [66] httpuv_1.6.15          future.apply_1.11.2    goftest_1.2-3          R.oo_1.26.0            glue_1.8.0            
 [71] dbscan_1.2-0           callr_3.7.6            nlme_3.1-164           promises_1.3.0         grid_4.4.0            
 [76] Rtsne_0.17             cluster_2.1.6          reshape2_1.4.4         generics_0.1.3         gtable_0.3.5          
 [81] spatstat.data_3.1-2    tzdb_0.4.0             R.methodsS3_1.8.2      data.table_1.15.4      hms_1.1.3             
 [86] sp_2.1-4               utf8_1.2.4             spatstat.geom_3.2-9    RcppAnnoy_0.0.22       ggrepel_0.9.5         
 [91] RANN_2.6.1             pillar_1.9.0           spam_2.10-0            RcppHNSW_0.6.0         later_1.3.2           
 [96] splines_4.4.0          lattice_0.22-6         deldir_2.0-4           survival_3.5-8         tidyselect_1.2.1      
[101] miniUI_0.1.1.1         pbapply_1.7-2          gridExtra_2.3          ggunchull_1.0.1        scattermore_1.2       
[106] devtools_2.4.5         matrixStats_1.3.0      stringi_1.8.4          lazyeval_0.2.2         codetools_0.2-20      
[111] interp_1.1-6           sgeostat_1.0-27        BiocManager_1.30.23    cli_3.6.2              alphahull_2.5         
[116] uwot_0.2.2             xtable_1.8-4           reticulate_1.38.0      munsell_0.5.1          processx_3.8.4        
[121] Rcpp_1.0.12            spatstat.random_3.2-3  globals_0.16.3         png_0.1-8              parallel_4.4.0        
[126] ellipsis_0.3.2         dotCall64_1.1-1        profvis_0.3.8          urlchecker_1.0.1       listenv_0.9.1         
[131] viridisLite_0.4.2      scales_1.3.0           ggridges_0.5.6         SeuratObject_5.0.2     leiden_0.4.3.1        
[136] rlang_1.1.4            cowplot_1.1.3

Best regards

[junjunlab]

I follow your code and I get a normal plot:

[junyitao5462]

I found ggrepel::geom_text_repel() has a conflict with ggplot2::coord_flip() and updated my ggrepel package from ggrepel_0.9.5 to 0.9.6 and solved the problem.