dotplot: wrong orderBy parameter; set to default `orderBy = "x"`

[sunta3iouxos]

The plot is created, but I have no idea on the error. I have a DEG set produced by DeSeq2. I get the sorted ranked with ENSEMBL names (hg38) as:

head(geneListDF)
ENSG00000256377 ENSG00000159713 ENSG00000176387 ENSG00000113296 ENSG00000174059 
       8.132732        6.644455        5.898174        5.744217        5.668175 
ENSG00000130592 
       5.475563

I generate the enriched list:

ego3 <- gseGO(geneList     = geneListDF,
              OrgDb        = org.Hs.eg.db,
              ont          = "BP",
              keyType = "ENSEMBL",
              minGSSize    = 100,
              maxGSSize    = 500,
              pvalueCutoff = 0.05,
              verbose      = FALSE)

then I try to produce the plot:

dotplot(ego3, showCategory=20)
wrong orderBy parameter; set to default `orderBy = "x"`

The plot is actually created, but I am wondered why this error.

ego3
#
# Gene Set Enrichment Analysis
#
#...@organism 	 Homo sapiens 
#...@setType 	 BP 
#...@keytype 	 ENSEMBL 
#...@geneList 	 Named num [1:32522] 8.13 6.64 5.9 5.74 5.67 ...
 - attr(*, "names")= chr [1:32522] "ENSG00000256377" "ENSG00000159713" "ENSG00000176387" "ENSG00000113296" ...
#...nPerm 	 
#...pvalues adjusted by 'BH' with cutoff <0.05 
#...831 enriched terms found
'data.frame':	831 obs. of  11 variables:
 $ ID             : chr  "GO:0000070" "GO:0000082" "GO:0000280" "GO:0000819" ...
 $ Description    : chr  "mitotic sister chromatid segregation" "G1/S transition of mitotic cell cycle" "nuclear division" "sister chromatid segregation" ...
 $ setSize        : int  160 254 408 188 194 270 154 183 317 157 ...
 $ enrichmentScore: num  -0.623 -0.474 -0.53 -0.612 -0.531 ...
 $ NES            : num  -2.6 -2.11 -2.48 -2.61 -2.28 ...
 $ pvalue         : num  1e-10 1e-10 1e-10 1e-10 1e-10 ...
 $ p.adjust       : num  3.24e-09 3.24e-09 3.24e-09 3.24e-09 3.24e-09 ...
 $ qvalues        : num  1.15e-09 1.15e-09 1.15e-09 1.15e-09 1.15e-09 ...
 $ rank           : num  5522 6746 5530 5857 5254 ...
 $ leading_edge   : chr  "tags=43%, list=17%, signal=36%" "tags=37%, list=21%, signal=29%" "tags=36%, list=17%, signal=30%" "tags=43%, list=18%, signal=35%" ...
 $ core_enrichment: chr  "ENSG00000085415/ENSG00000121579/ENSG00000108424/ENSG00000198887/ENSG00000149636/ENSG00000168802/ENSG00000132341"| __truncated__ "ENSG00000131023/ENSG00000149308/ENSG00000162676/ENSG00000169016/ENSG00000156273/ENSG00000253729/ENSG00000150457"| __truncated__ "ENSG00000154429/ENSG00000085415/ENSG00000121579/ENSG00000139351/ENSG00000134278/ENSG00000108424/ENSG00000105173"| __truncated__ "ENSG00000197771/ENSG00000198824/ENSG00000062650/ENSG00000116560/ENSG00000085415/ENSG00000121579/ENSG00000108424"| __truncated__ ...
#...Citation
  Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.
  clusterProfiler: an R package for comparing biological themes among
  gene clusters. OMICS: A Journal of Integrative Biology
  2012, 16(5):284-287 

Any ideas?

My session:

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252   
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

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

other attached packages:
 [1] enrichplot_1.10.2           manhattanly_0.3.0          
 [3] heatmaply_1.3.0             viridis_0.6.2              
 [5] viridisLite_0.4.0           plotly_4.10.0              
 [7] writexl_1.4.0               pathview_1.30.1            
 [9] biomaRt_2.46.3              AnnotationHub_2.22.1       
[11] BiocFileCache_1.14.0        dbplyr_2.1.1               
[13] org.Hs.eg.db_3.12.0         AnnotationDbi_1.52.0       
[15] plyr_1.8.6                  clusterProfiler_3.18.1     
[17] ggrepel_0.9.1               ggplot2_3.3.5              
[19] pheatmap_1.0.12             RColorBrewer_1.1-2         
[21] DESeq2_1.30.1               SummarizedExperiment_1.20.0
[23] Biobase_2.50.0              MatrixGenerics_1.2.1       
[25] matrixStats_0.61.0          GenomicRanges_1.42.0       
[27] GenomeInfoDb_1.26.7         IRanges_2.24.1             
[29] S4Vectors_0.28.1            BiocGenerics_0.36.1        

loaded via a namespace (and not attached):
  [1] snow_0.4-4                    shadowtext_0.1.1             
  [3] fastmatch_1.1-3               igraph_1.2.11                
  [5] lazyeval_0.2.2                splines_4.0.3                
  [7] crosstalk_1.2.0               BiocParallel_1.24.1          
  [9] digest_0.6.29                 foreach_1.5.2                
 [11] yulab.utils_0.0.4             htmltools_0.5.2              
 [13] GOSemSim_2.16.1               GO.db_3.12.1                 
 [15] fansi_1.0.2                   magrittr_2.0.2               
 [17] memoise_2.0.1                 tzdb_0.2.0                   
 [19] Biostrings_2.58.0             annotate_1.68.0              
 [21] graphlayouts_0.8.0            vroom_1.5.7                  
 [23] askpass_1.1                   prettyunits_1.1.1            
 [25] colorspace_2.0-2              blob_1.2.2                   
 [27] rappdirs_0.3.3                xfun_0.29                    
 [29] dplyr_1.0.8                   crayon_1.5.0                 
 [31] RCurl_1.98-1.6                jsonlite_1.7.3               
 [33] graph_1.68.0                  scatterpie_0.1.7             
 [35] genefilter_1.72.1             iterators_1.0.14             
 [37] survival_3.2-7                glue_1.6.1                   
 [39] polyclip_1.10-0               registry_0.5-1               
 [41] gtable_0.3.0                  zlibbioc_1.36.0              
 [43] XVector_0.30.0                webshot_0.5.2                
 [45] DelayedArray_0.16.3           Rgraphviz_2.34.0             
 [47] scales_1.1.1                  DOSE_3.16.0                  
 [49] DBI_1.1.2                     Rcpp_1.0.8                   
 [51] xtable_1.8-4                  progress_1.2.2               
 [53] bit_4.0.4                     htmlwidgets_1.5.4            
 [55] httr_1.4.2                    fgsea_1.16.0                 
 [57] ellipsis_0.3.2                pkgconfig_2.0.3              
 [59] XML_3.99-0.8                  farver_2.1.0                 
 [61] locfit_1.5-9.4                utf8_1.2.2                   
 [63] tidyselect_1.1.1              labeling_0.4.2               
 [65] rlang_1.0.1                   reshape2_1.4.4               
 [67] later_1.3.0                   munsell_0.5.0                
 [69] BiocVersion_3.12.0            tools_4.0.3                  
 [71] cachem_1.0.6                  downloader_0.4               
 [73] cli_3.2.0                     generics_0.1.2               
 [75] RSQLite_2.2.10                stringr_1.4.0                
 [77] fastmap_1.1.0                 yaml_2.3.4                   
 [79] bit64_4.0.5                   tidygraph_1.2.0              
 [81] purrr_0.3.4                   dendextend_1.15.2            
 [83] KEGGREST_1.30.1               ggraph_2.0.5                 
 [85] mime_0.12                     KEGGgraph_1.50.0             
 [87] DO.db_2.9                     xml2_1.3.3                   
 [89] compiler_4.0.3                rstudioapi_0.13              
 [91] png_0.1-7                     curl_4.3.2                   
 [93] interactiveDisplayBase_1.28.0 tibble_3.1.6                 
 [95] tweenr_1.0.2                  geneplotter_1.68.0           
 [97] stringi_1.7.6                 lattice_0.20-41              
 [99] Matrix_1.4-0                  vctrs_0.3.8                  
[101] pillar_1.7.0                  lifecycle_1.0.1              
[103] BiocManager_1.30.16           data.table_1.14.2            
[105] cowplot_1.1.1                 bitops_1.0-7                 
[107] seriation_1.3.2               httpuv_1.6.5                 
[109] qvalue_2.22.0                 R6_2.5.1                     
[111] TSP_1.1-11                    promises_1.2.0.1             
[113] gridExtra_2.3                 codetools_0.2-16             
[115] MASS_7.3-53                   assertthat_0.2.1             
[117] openssl_1.4.6                 withr_2.4.3                  
[119] GenomeInfoDbData_1.2.4        hms_1.1.1                    
[121] grid_4.0.3                    ggfun_0.0.5                  
[123] tidyr_1.2.0                   rvcheck_0.2.1                
[125] ggforce_0.3.3                 shiny_1.7.1                  
[127] tinytex_0.37

[huerqiang]

This had been fixed by the release version of enrichplot.

[sunta3iouxos]

I am a bit confused. How do I update to the latest version? Am I using the:

library(remotes)
install_github(c("GuangchuangYu/DOSE", "GuangchuangYu/clusterProfiler", "GuangchuangYu/enrichplot" ))

or something else?this might be relevant #434 Thank you!