cnetplot error: Problem while computing aesthetics. Error occurred in the 5th layer. #315
Description
Hi,
I got an error when using cnetplot
# plot hallmark pathways
> cnetplot(ora.H)
Error:
! Problem while computing aesthetics.
ℹ Error occurred in the 5th layer.
Caused by error in `.data$x`:
! Column `x` not found in `.data`.
Backtrace:
1. base (local) `<fn>`(x)
20. rlang:::abort_data_pronoun(x, call = y)here's the session info
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
attached base packages:
[1] stats4 grid stats graphics grDevices datasets utils methods base
other attached packages:
[1] limma_3.58.1 ggVennDiagram_1.5.2 ggvenn_0.1.10 UpSetR_1.4.0 GenomicDistributions_1.10.0
[6] GenomicRanges_1.54.1 GenomeInfoDb_1.38.1 enrichR_3.2 org.Hs.eg.db_3.18.0 AnnotationDbi_1.64.1
[11] IRanges_2.36.0 S4Vectors_0.40.1 Biobase_2.62.0 BiocGenerics_0.48.1 clusterProfiler_4.10.1
[16] Seurat_5.0.1 SeuratObject_5.0.1 sp_2.1-2 cowplot_1.1.1 patchwork_1.3.0.9000
[21] ggpubr_0.6.0 ggrepel_0.9.4 ggrastr_1.0.2 scattermore_1.2 pheatmap_1.0.12
[26] ComplexHeatmap_2.18.0 scales_1.3.0 RColorBrewer_1.1-3 ggsci_3.0.0 data.table_1.14.8
[31] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[36] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
[41] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] R.methodsS3_1.8.2 vroom_1.6.5 goftest_1.2-3 DT_0.30 Biostrings_2.70.1
[6] vctrs_0.6.5 ggtangle_0.0.6 spatstat.random_3.2-2 RApiSerialize_0.1.4 digest_0.6.33
[11] png_0.1-8 shape_1.4.6 git2r_0.33.0 deldir_2.0-2 parallelly_1.36.0
[16] renv_1.0.3 magick_2.8.1 MASS_7.3-60.0.1 reshape2_1.4.4 httpuv_1.6.13
[21] foreach_1.5.2 qvalue_2.34.0 withr_2.5.2 xfun_0.40 ggfun_0.1.8
[26] ellipsis_0.3.2 survival_3.5-7 memoise_2.0.1 ggbeeswarm_0.7.2 gson_0.1.0
[31] systemfonts_1.0.5 ragg_1.2.6 tidytree_0.4.6 zoo_1.8-12 GlobalOptions_0.1.2
[36] pbapply_1.7-2 R.oo_1.25.0 KEGGREST_1.42.0 promises_1.2.1 httr_1.4.7
[41] rstatix_0.7.2 globals_0.16.2 fitdistrplus_1.1-11 ps_1.7.5 stringfish_0.16.0
[46] rstudioapi_0.15.0 miniUI_0.1.1.1 generics_0.1.3 DOSE_4.1.0 processx_3.8.2
[51] curl_5.1.0 zlibbioc_1.48.0 polyclip_1.10-6 GenomeInfoDbData_1.2.11 xtable_1.8-4
[56] doParallel_1.0.17 evaluate_0.23 hms_1.1.3 irlba_2.3.5.1 qs_0.27.2
[61] colorspace_2.1-0 ROCR_1.0-11 reticulate_1.34.0 spatstat.data_3.0-3 magrittr_2.0.3
[66] lmtest_0.9-40 later_1.3.2 ggtree_3.10.0 lattice_0.22-6 spatstat.geom_3.2-7
[71] future.apply_1.11.0 getPass_0.2-2 matrixStats_1.1.0 RcppAnnoy_0.0.21 pillar_1.9.0
[76] nlme_3.1-163 iterators_1.0.14 compiler_4.3.2 RSpectra_0.16-1 stringi_1.8.2
[81] tensor_1.5 plyr_1.8.9 crayon_1.5.2 abind_1.4-5 gridGraphics_0.5-1
[86] bit_4.0.5 fastmatch_1.1-4 whisker_0.4.1 codetools_0.2-20 textshaping_0.3.7
[91] crosstalk_1.2.1 bslib_0.6.1 GetoptLong_1.0.5 plotly_4.10.3 mime_0.12
[96] splines_4.3.2 circlize_0.4.15 Rcpp_1.0.14 fastDummies_1.7.3 knitr_1.44
[101] blob_1.2.4 utf8_1.2.3 here_1.0.1 clue_0.3-65 WriteXLS_6.7.0
[106] fs_1.6.3 listenv_0.9.0 ggsignif_0.6.4 ggplotify_0.1.2 Matrix_1.6-4
[111] callr_3.7.3 statmod_1.5.0 tzdb_0.4.0 tweenr_2.0.2 pkgconfig_2.0.3
[116] tools_4.3.2 cachem_1.0.8 RSQLite_2.3.4 viridisLite_0.4.2 DBI_1.1.3
[121] fastmap_1.1.1 rmarkdown_2.25 ica_1.0-3 broom_1.0.5 sass_0.4.8
[126] dotCall64_1.1-1 carData_3.0-5 RANN_2.6.1 farver_2.1.1 scatterpie_0.2.4
[131] yaml_2.3.7 cli_3.6.1 leiden_0.4.3.1 lifecycle_1.0.3 uwot_0.1.16
[136] backports_1.4.1 BiocParallel_1.36.0 timechange_0.2.0 gtable_0.3.4 rjson_0.2.21
[141] ggridges_0.5.4 progressr_0.14.0 parallel_4.3.2 ape_5.7-1 jsonlite_1.8.8
[146] RcppHNSW_0.5.0 bitops_1.0-7 bit64_4.0.5 Rtsne_0.17 yulab.utils_0.1.7.001
[151] spatstat.utils_3.1-0 RcppParallel_5.1.10 jquerylib_0.1.4 GOSemSim_2.33.0 R.utils_2.12.3
[156] lazyeval_0.2.2 shiny_1.8.0 htmltools_0.5.7 enrichplot_1.27.4.001 GO.db_3.18.0
[161] sctransform_0.4.1 glue_1.6.2 spam_2.10-0 XVector_0.42.0 RCurl_1.98-1.13
[166] rprojroot_2.0.4 treeio_1.31.0 gridExtra_2.3 igraph_1.5.1 R6_2.5.1
[171] labeling_0.4.3 cluster_2.1.4 aplot_0.2.2 tidyselect_1.2.0 vipor_0.4.5
[176] ggforce_0.4.1 car_3.1-2 future_1.33.0 munsell_0.5.0 KernSmooth_2.23-24
[181] htmlwidgets_1.6.2 fgsea_1.28.0 rlang_1.1.4 spatstat.sparse_3.0-3 spatstat.explore_3.2-5
[186] fansi_1.0.4 Cairo_1.6-2 beeswarm_0.4.0Thanks for your help!