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20 hours ago •
YuLab-SMU
YuLab-SMU
Error: How to solve the fact that goplot keeps asking for text input?
Hi there,
I aim to goplot() ego output, but it keeps giving me a "?" asking for some text input as below. What is interesting was the ego object egoGOEnrichGeneSet has nothing to do with geneList_FCsorted_OmitNA_gseGO_termsim in the error.
enrichplot::goplot(egoGOEnrichGeneSet)
Error in parse(text = Ancestors) : <stdin>:1:3: unexpected input
0: base::suppressWarnings(base::try(geneList_FCsorted_OmitNA_gseGO_termsim$Description, silent = TRUE))
1: XT
^
> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /Filers/package/R-base/4.2.0/lib64/R/lib/libRblas.so
LAPACK: /Filers/package/R-base/4.2.0/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] DOSE_3.22.0 enrichplot_1.16.1 clusterProfiler_4.4.4 org.Hs.eg.db_3.15.0 AnnotationDbi_1.58.0
[6] IRanges_2.30.0 S4Vectors_0.34.0 Biobase_2.56.0 BiocGenerics_0.42.0 pbmc3k.SeuratData_3.1.4
[11] ifnb.SeuratData_3.1.0 SeuratData_0.2.1 SeuratWrappers_0.3.0 sp_1.5-0 SeuratObject_4.1.0
[16] Seurat_4.1.1 tidyr_1.2.0 viridis_0.6.2 viridisLite_0.4.0 gridExtra_2.3
[21] scRepertoire_1.6.0 ggplot2_3.3.6
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 SparseM_1.81 scattermore_0.8 R.methodsS3_1.8.1
[5] evmix_2.12 bit64_4.0.5 irlba_2.3.5 DelayedArray_0.22.0
[9] R.utils_2.11.0 data.table_1.14.2 rpart_4.1.16 KEGGREST_1.36.0
[13] RCurl_1.98-1.6 doParallel_1.0.17 generics_0.1.2 callr_3.7.0
[17] cowplot_1.1.1 usethis_2.1.6 RSQLite_2.2.14 shadowtext_0.1.2
[21] RANN_2.6.1 VGAM_1.1-6 future_1.26.1 bit_4.0.4
[25] spatstat.data_2.2-0 httpuv_1.6.5 SummarizedExperiment_1.26.1 assertthat_0.2.1
[29] promises_1.2.0.1 fansi_1.0.3 igraph_1.3.1 DBI_1.1.2
[33] htmlwidgets_1.5.4 powerTCR_1.16.0 spatstat.geom_2.4-0 stringdist_0.9.8
[37] purrr_0.3.4 ellipsis_0.3.2 dplyr_1.0.9 permute_0.9-7
[41] deldir_1.0-6 MatrixGenerics_1.8.0 vctrs_0.4.1 ggalluvial_0.12.3
[45] remotes_2.4.2 ROCR_1.0-11 abind_1.4-5 cachem_1.0.6
[49] withr_2.5.0 ggforce_0.3.3 progressr_0.10.1 sctransform_0.3.3
[53] vegan_2.6-2 treeio_1.20.0 prettyunits_1.1.1 goftest_1.2-3
[57] cluster_2.1.3 gsl_2.1-7.1 ape_5.6-2 lazyeval_0.2.2
[61] crayon_1.5.1 pkgconfig_2.0.3 tweenr_1.0.2 GenomeInfoDb_1.32.2
[65] nlme_3.1-157 pkgload_1.3.0 devtools_2.4.3 rlang_1.0.3
[69] globals_0.15.0 lifecycle_1.0.1 miniUI_0.1.1.1 downloader_0.4
[73] rsvd_1.0.5 polyclip_1.10-0 matrixStats_0.62.0 lmtest_0.9-40
[77] Matrix_1.4-1 aplot_0.1.6 zoo_1.8-10 ggridges_0.5.3
[81] GlobalOptions_0.1.2 processx_3.7.0 png_0.1-7 bitops_1.0-7
[85] R.oo_1.24.0 KernSmooth_2.23-20 Biostrings_2.64.0 blob_1.2.3
[89] shape_1.4.6 stringr_1.4.0 qvalue_2.28.0 parallelly_1.32.0
[93] spatstat.random_2.2-0 gridGraphics_0.5-1 scales_1.2.0 memoise_2.0.1
[97] magrittr_2.0.3 plyr_1.8.7 ica_1.0-2 zlibbioc_1.42.0
[101] compiler_4.2.0 scatterpie_0.1.7 RColorBrewer_1.1-3 fitdistrplus_1.1-8
[105] cli_3.3.0 XVector_0.36.0 listenv_0.8.0 patchwork_1.1.1
[109] pbapply_1.5-0 ps_1.7.1 MASS_7.3-57 mgcv_1.8-40
[113] tidyselect_1.1.2 stringi_1.7.6 GOSemSim_2.22.0 ggrepel_0.9.1
[117] fastmatch_1.1-3 tools_4.2.0 future.apply_1.9.0 parallel_4.2.0
[121] circlize_0.4.15 rstudioapi_0.13 foreach_1.5.2 cubature_2.0.4.4
[125] farver_2.1.1 Rtsne_0.16 ggraph_2.0.5 digest_0.6.29
[129] BiocManager_1.30.18 rgeos_0.5-9 shiny_1.7.1 Rcpp_1.0.8.3
[133] GenomicRanges_1.48.0 later_1.3.0 RcppAnnoy_0.0.19 httr_1.4.3
[137] colorspace_2.0-3 fs_1.5.2 tensor_1.5 reticulate_1.25
[141] splines_4.2.0 uwot_0.1.11 yulab.utils_0.0.5 tidytree_0.3.9
[145] spatstat.utils_2.3-1 graphlayouts_0.8.0 ggplotify_0.1.0 plotly_4.10.0
[149] sessioninfo_1.2.2 xtable_1.8-4 jsonlite_1.8.0 ggtree_3.4.0
[153] truncdist_1.0-2 tidygraph_1.2.1 ggfun_0.0.6 R6_2.5.1
[157] pillar_1.7.0 htmltools_0.5.2 mime_0.12 glue_1.6.2
[161] fastmap_1.1.0 BiocParallel_1.30.3 codetools_0.2-18 fgsea_1.22.0
[165] pkgbuild_1.3.1 utf8_1.2.2 lattice_0.20-45 spatstat.sparse_2.1-1
[169] tibble_3.1.7 evd_2.3-6 leiden_0.4.2 GO.db_3.15.0
[173] survival_3.3-1 munsell_0.5.0 DO.db_2.9 GenomeInfoDbData_1.2.8
[177] iterators_1.0.14 reshape2_1.4.4 gtable_0.3.0 spatstat.core_2.4-4
Me too.
> goplot(cprof.up.bp.fisher, showCategory = 10)
?;
Error in parse(text = Ancestors) : <stdin>:1:1: unexpected ';'
1: ;
^
>
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] GO.db_3.16.0 AnnotationDbi_1.60.2 IRanges_2.32.0 S4Vectors_0.36.2
[5] Biobase_2.58.0 BiocGenerics_0.44.0 clusterProfiler_4.6.2
loaded via a namespace (and not attached):
[1] nlme_3.1-162 bitops_1.0-7 ggtree_3.6.2 enrichplot_1.18.4
[5] bit64_4.0.5 HDO.db_0.99.1 RColorBrewer_1.1-3 httr_1.4.6
[9] GenomeInfoDb_1.34.9 tools_4.2.2 utf8_1.2.3 R6_2.5.1
[13] lazyeval_0.2.2 DBI_1.1.3 colorspace_2.1-0 withr_2.5.0
[17] tidyselect_1.2.0 gridExtra_2.3 bit_4.0.5 compiler_4.2.2
[21] cli_3.6.1 scatterpie_0.2.1 shadowtext_0.1.2 scales_1.2.1
[25] stringr_1.5.0 digest_0.6.31 yulab.utils_0.0.6 gson_0.1.0
[29] DOSE_3.24.2 XVector_0.38.0 pkgconfig_2.0.3 fastmap_1.1.1
[33] rlang_1.1.1 RSQLite_2.3.1 gridGraphics_0.5-1 farver_2.1.1
[37] generics_0.1.3 jsonlite_1.8.7 BiocParallel_1.32.6 GOSemSim_2.24.0
[41] dplyr_1.1.2 RCurl_1.98-1.12 magrittr_2.0.3 ggplotify_0.1.1
[45] GenomeInfoDbData_1.2.9 patchwork_1.1.2 Matrix_1.5-4.1 Rcpp_1.0.11
[49] munsell_0.5.0 fansi_1.0.4 ape_5.7-1 viridis_0.6.3
[53] lifecycle_1.0.3 stringi_1.7.12 ggraph_2.1.0 MASS_7.3-60
[57] zlibbioc_1.44.0 plyr_1.8.8 qvalue_2.30.0 grid_4.2.2
[61] blob_1.2.4 parallel_4.2.2 ggrepel_0.9.3 crayon_1.5.2
[65] lattice_0.21-8 graphlayouts_1.0.0 Biostrings_2.66.0 cowplot_1.1.1
[69] splines_4.2.2 KEGGREST_1.38.0 pillar_1.9.0 fgsea_1.24.0
[73] igraph_1.5.0 reshape2_1.4.4 codetools_0.2-19 fastmatch_1.1-3
[77] glue_1.6.2 ggfun_0.1.1 downloader_0.4 data.table_1.14.8
[81] treeio_1.22.0 png_0.1-8 vctrs_0.6.3 tweenr_2.0.2
[85] gtable_0.3.3 purrr_1.0.1 polyclip_1.10-4 tidyr_1.3.0
[89] cachem_1.0.8 ggplot2_3.4.2 ggforce_0.4.1 tidygraph_1.2.3
[93] tidytree_0.4.2 viridisLite_0.4.2 tibble_3.2.1 aplot_0.1.10
[97] memoise_2.0.1
>
In my case, I found the fix is as follows, after comparison of this object of enricher() with that of enrichGO() with which goplot works.
cprof.up.bp.fisher@ontology <- "BP"
# for test result of data with ontology 'BP' among ontology type BP/MF/CC
goplot(cprof.up.bp.fisher, showCategory = 10)
> goplot(cprof.up.bp.fisher, showCategory = 10)
?BP
Error in eval(parse(text = Ancestors)) : object 'BP' not found
> goplot(cprof.up.bp.fisher, showCategory = 10)
?"BP"
Error in AnnotationDbi::mget(id, GOANCESTOR) :
second argument must be an environment
>
> cprof.up.bp.fisher@ontology
[1] "UNKNOWN"
> cprof.up.bp.fisher@ontology <- "BP"
> cprof.up.bp.fisher@ontology
[1] "BP"
> goplot(cprof.up.bp.fisher, showCategory = 10)
>