ridgeplot error

[kaji331]

A gseaResult object generated by gsePathway function in ReactomePA could be accepted by ridgeplot function. But if you use the setReadable function to deal this gseaResult object, the ridgeplot function will throw an error for this new object:

Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : replacement has length zero In addition: Warning message: In rep(yes, length.out = len) : 'x' is NULL so the result will be NULL

--- SessionInfo --- R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] C

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

other attached packages: [1] pathview_1.34.0 pipeR_0.6.1.3 enrichplot_1.14.2 ggsci_2.9
[5] ggplot2_3.3.5 org.Hs.eg.db_3.14.0 DOSE_3.20.1 clusterProfiler_4.2.2
[9] org.Mm.eg.db_3.14.0 AnnotationDbi_1.56.2 IRanges_2.28.0 S4Vectors_0.32.4
[13] Biobase_2.54.0 BiocGenerics_0.40.0 modules_0.10.0 shinydashboardPlus_2.0.3 [17] shinydashboard_0.7.2 shinythemes_1.2.0 shiny_1.7.1

loaded via a namespace (and not attached): [1] utf8_1.2.2 tidyselect_1.1.2 heatmaply_1.3.0
[4] RSQLite_2.2.11 htmlwidgets_1.5.4 grid_4.1.2
[7] TSP_1.2-0 BiocParallel_1.28.3 scatterpie_0.1.7
[10] munsell_0.5.0 codetools_0.2-18 DT_0.22
[13] withr_2.5.0 colorspace_2.0-3 GOSemSim_2.20.0
[16] rstudioapi_0.13 labeling_0.4.2 MatrixGenerics_1.6.0
[19] KEGGgraph_1.54.0 GenomeInfoDbData_1.2.7 polyclip_1.10-0
[22] bit64_4.0.5 farver_2.1.0 downloader_0.4
[25] vctrs_0.4.0 treeio_1.18.1 generics_0.1.2
[28] TH.data_1.1-0 ggthemes_4.2.4 R6_2.5.1
[31] doParallel_1.0.17 GenomeInfoDb_1.30.1 clue_0.3-60
[34] graphlayouts_0.8.0 seriation_1.3.5 locfit_1.5-9.5
[37] bitops_1.0-7 cachem_1.0.6 fgsea_1.20.0
[40] gridGraphics_0.5-1 DelayedArray_0.20.0 assertthat_0.2.1
[43] promises_1.2.0.1 shinycssloaders_1.0.0 scales_1.1.1
[46] multcomp_1.4-18 ggraph_2.0.5 gtable_0.3.0
[49] tidygraph_1.2.0 sandwich_3.0-1 rlang_1.0.2
[52] genefilter_1.76.0 FSA_0.9.3 GlobalOptions_0.1.2
[55] splines_4.1.2 lazyeval_0.2.2 checkmate_2.0.0
[58] yaml_2.3.5 reshape2_1.4.4 crosstalk_1.2.0
[61] backports_1.4.1 httpuv_1.6.5 qvalue_2.26.0
[64] tools_4.1.2 ggplotify_0.1.0 ellipsis_0.3.2
[67] jquerylib_0.1.4 RColorBrewer_1.1-2 ggridges_0.5.3
[70] Rcpp_1.0.8.3 plyr_1.8.7 zlibbioc_1.40.0
[73] purrr_0.3.4 RCurl_1.98-1.6 GetoptLong_1.0.5
[76] viridis_0.6.2 fontawesome_0.2.2 zoo_1.8-9
[79] cluster_2.1.3 SummarizedExperiment_1.24.0 ggrepel_0.9.1
[82] magrittr_2.0.3 data.table_1.14.2 DO.db_2.9
[85] circlize_0.4.14 reactome.db_1.77.0 mvtnorm_1.1-3
[88] ggnewscale_0.4.7 matrixStats_0.61.0 patchwork_1.1.1
[91] mime_0.12 xtable_1.8-4 XML_3.99-0.9
[94] shape_1.4.6 gridExtra_2.3 ggupset_0.3.0
[97] compiler_4.1.2 tibble_3.1.6 crayon_1.5.1
[100] shadowtext_0.1.1 htmltools_0.5.2 ggfun_0.0.5
[103] later_1.3.0 tidyr_1.2.0 geneplotter_1.72.0
[106] aplot_0.1.3 ReactomePA_1.38.0 DBI_1.1.2
[109] tweenr_1.0.2 ComplexHeatmap_2.10.0 MASS_7.3-56
[112] rappdirs_0.3.3 Matrix_1.4-1 cli_3.2.0
[115] parallel_4.1.2 igraph_1.2.11 GenomicRanges_1.46.1
[118] pkgconfig_2.0.3 registry_0.5-1 plotly_4.10.0
[121] foreach_1.5.2 ggtree_3.2.1 annotate_1.72.0
[124] bslib_0.3.1 webshot_0.5.2 XVector_0.34.0
[127] yulab.utils_0.0.4 stringr_1.4.0 digest_0.6.29
[130] graph_1.72.0 Biostrings_2.62.0 fastmatch_1.1-3
[133] tidytree_0.3.9 dendextend_1.15.2 graphite_1.40.0
[136] rjson_0.2.21 lifecycle_1.0.1 nlme_3.1-157
[139] jsonlite_1.8.0 viridisLite_0.4.0 fansi_1.0.3
[142] pillar_1.7.0 lattice_0.20-45 KEGGREST_1.34.0
[145] fastmap_1.1.0 httr_1.4.2 survival_3.3-1
[148] GO.db_3.14.0 glue_1.6.2 png_0.1-7
[151] iterators_1.0.14 bit_4.0.4 Rgraphviz_2.38.0
[154] ggforce_0.3.3 stringi_1.7.6 sass_0.4.1
[157] blob_1.2.2 DESeq2_1.34.0 memoise_2.0.1
[160] dplyr_1.0.8 ape_5.6-2

[kaji331]

I checked all gseaResult generated by other functions (e.g. gseGO, gseKEGG, gseMKEGG) would be refused by ridgeplot function after setReadable.

[kaji331]

again, upsetplot has a similar error!