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dotplot() error after compareCluster() for fun = "groupGO" with data(gcSample)

Open sunta3iouxos opened this issue 9 months ago • 1 comments

Describe your issue

Even using the example from the documentation I am getting errors:

> xx <- enrichplot::pairwise_termsim(xx)                     
> clusterProfiler::dotplot(xx)
> xx <- compareCluster(gcSample,
+                fun = "groupGO",
+                OrgDb= 'org.Hs.eg.db',
+                ont           = "BP",
+                readable      = TRUE)
> clusterProfiler::dotplot(xx)
Error in `geom_point()`:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `compute_aesthetics()`:
! Aesthetics are not valid data columns.
✖ The following aesthetics are invalid:
✖ `colour = p.adjust`
ℹ Did you mistype the name of a data column or forget to add `after_stat()`?
Run `rlang::last_trace()` to see where the error occurred.

But enrichKEGG and enrichGO works as expected

data(gcSample)
xx <- compareCluster(gcSample, fun="enrichKEGG",
                     organism="hsa", pvalueCutoff=0.05)
xx <- enrichplot::pairwise_termsim(xx)                     
clusterProfiler::dotplot(xx)
Warning messages:
1: In utils::download.file(url, quiet = TRUE, method = method, ...) :
  the 'wininet' method is deprecated for http:// and https:// URLs
2: In utils::download.file(url, quiet = TRUE, method = method, ...) :
  the 'wininet' method is deprecated for http:// and https:// URLs

sessioninfo:

> 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    LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.utf8    

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

other attached packages:
 [1] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 GenomicFeatures_1.50.4                   
 [3] GenomicRanges_1.50.2                      GenomeInfoDb_1.34.9                      
 [5] clusterProfiler_4.6.2                     org.Mm.eg.db_3.16.0                      
 [7] AnnotationDbi_1.60.2                      IRanges_2.32.0                           
 [9] S4Vectors_0.36.2                          Biobase_2.58.0                           
[11] BiocGenerics_0.44.0                      

loaded via a namespace (and not attached):
  [1] shadowtext_0.1.2            fastmatch_1.1-3             BiocFileCache_2.6.1         plyr_1.8.8                 
  [5] igraph_1.4.2                lazyeval_0.2.2              splines_4.2.2               BiocParallel_1.32.6        
  [9] pathview_1.38.0             ggplot2_3.4.2               digest_0.6.31               yulab.utils_0.0.6          
 [13] GOSemSim_2.24.0             viridis_0.6.2               GO.db_3.16.0                fansi_1.0.4                
 [17] magrittr_2.0.3              memoise_2.0.1               Biostrings_2.66.0           graphlayouts_0.8.4         
 [21] matrixStats_0.63.0          enrichplot_1.18.3           prettyunits_1.1.1           colorspace_2.1-0           
 [25] blob_1.2.4                  rappdirs_0.3.3              ggrepel_0.9.3               dplyr_1.1.2                
 [29] crayon_1.5.2                RCurl_1.98-1.12             jsonlite_1.8.4              graph_1.76.0               
 [33] scatterpie_0.1.8            ape_5.7-1                   glue_1.6.2                  polyclip_1.10-4            
 [37] gtable_0.3.3                zlibbioc_1.44.0             XVector_0.38.0              DelayedArray_0.24.0        
 [41] graphite_1.44.0             Rgraphviz_2.42.0            scales_1.2.1                DOSE_3.24.2                
 [45] futile.options_1.0.1        DBI_1.1.3                   Rcpp_1.0.10                 viridisLite_0.4.1          
 [49] progress_1.2.2              gridGraphics_0.5-1          tidytree_0.4.2              bit_4.0.5                  
 [53] reactome.db_1.82.0          httr_1.4.5                  fgsea_1.24.0                RColorBrewer_1.1-3         
 [57] pkgconfig_2.0.3             XML_3.99-0.14               farver_2.1.1                dbplyr_2.3.2               
 [61] utf8_1.2.3                  ggplotify_0.1.0             tidyselect_1.2.0            labeling_0.4.2             
 [65] rlang_1.1.0                 reshape2_1.4.4              munsell_0.5.0               tools_4.2.2                
 [69] cachem_1.0.7                downloader_0.4              cli_3.6.0                   generics_0.1.3             
 [73] RSQLite_2.3.0               gson_0.1.0                  stringr_1.5.0               fastmap_1.1.1              
 [77] yaml_2.3.7                  ggtree_3.6.2                org.Hs.eg.db_3.16.0         bit64_4.0.5                
 [81] tidygraph_1.2.3             purrr_1.0.1                 KEGGREST_1.38.0             ggraph_2.1.0               
 [85] ReactomePA_1.42.0           nlme_3.1-160                formatR_1.14                KEGGgraph_1.58.3           
 [89] aplot_0.1.10                xml2_1.3.3                  biomaRt_2.54.1              compiler_4.2.2             
 [93] rstudioapi_0.14             filelock_1.0.2              curl_5.0.0                  png_0.1-8                  
 [97] treeio_1.22.0               tibble_3.2.1                tweenr_2.0.2                stringi_1.7.12             
[101] futile.logger_1.4.3         lattice_0.21-8              Matrix_1.5-3                vctrs_0.6.0                
[105] pillar_1.9.0                lifecycle_1.0.3             data.table_1.14.8           cowplot_1.1.1              
[109] bitops_1.0-7                patchwork_1.1.2             rtracklayer_1.58.0          qvalue_2.30.0              
[113] R6_2.5.1                    BiocIO_1.8.0                gridExtra_2.3               codetools_0.2-18           
[117] lambda.r_1.2.4              MASS_7.3-58.3               SummarizedExperiment_1.28.0 rjson_0.2.21               
[121] withr_2.5.0                 GenomicAlignments_1.34.1    Rsamtools_2.14.0            GenomeInfoDbData_1.2.9     
[125] parallel_4.2.2              hms_1.1.3                   VennDiagram_1.7.3           grid_4.2.2                 
[129] ggfun_0.0.9                 tidyr_1.3.0                 HDO.db_0.99.1               MatrixGenerics_1.10.0      
[133] ggforce_0.4.1               restfulr_0.0.15     

sunta3iouxos avatar Nov 13 '23 14:11 sunta3iouxos