Open nick-youngblut opened 1 year ago
Regardless of the layout that I set for visIgraphLayout(), I get the following error:
visIgraphLayout()
Error in `[.data.frame`(graph$x$nodes, , c("id", setdiff(names(graph$x$nodes), : undefined columns selected 8. stop("undefined columns selected") 7. `[.data.frame`(graph$x$nodes, , c("id", setdiff(names(graph$x$nodes), "id"))) 6. graph$x$nodes[, c("id", setdiff(names(graph$x$nodes), "id"))] 5. igraph::graph_from_data_frame(graph$x$edges[, c("from", "to")], directed = TRUE, vertices = graph$x$nodes[, c("id", setdiff(names(graph$x$nodes), "id"))]) 4. visIgraphLayout(., layout = "layout_nicely") 3. visNetwork(nodes, edges, width = "100%") %>% visPhysics(stabilization = FALSE) %>% visEdges(smooth = FALSE) %>% visIgraphLayout(layout = "layout_nicely")
It appears to be some issue with the graph structure that only comes into play when I use visIgraphLayout() with visNetwork()
visNetwork()
R version 4.2.1 (2022-06-23) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.6 Matrix products: default 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] stats graphics grDevices datasets utils methods base other attached packages: [1] aws.signature_0.6.0 aws.s3_0.3.21 httr_1.4.4 visNetwork_2.1.2 tidygraph_1.2.2 [6] styler_1.8.1 lintr_3.0.2 languageserver_0.3.14 ggrepel_0.9.2 ggtree_3.6.2 [11] tidytree_0.4.1 treeio_1.22.0 ape_5.6-2 data.tree_1.0.0 lubridate_1.9.0 [16] timechange_0.1.1 memoise_2.0.1 tidytable_0.9.1 data.table_1.14.6 plotly_4.10.1 [21] ggplot2_3.4.0 reactable_0.3.0 collapsibleTree_0.1.7 shinyTree_0.2.7 shinyWidgets_0.7.5 [26] shinycssloaders_1.0.0 shinyBS_0.61.1 jsonlite_1.8.3 paws_0.1.12 dbplyr_2.2.1 [31] dplyr_1.0.10 DBI_1.1.3 shiny_1.7.3 RPostgres_1.4.4 loaded via a namespace (and not attached): [1] colorspace_2.0-3 ellipsis_0.3.2 rprojroot_2.0.3 base64enc_0.1-3 [5] aplot_0.1.8 paws.security.identity_0.1.12 farver_2.1.1 graphlayouts_0.8.4 [9] remotes_2.4.2 bit64_4.0.5 fansi_1.0.3 xml2_1.3.3 [13] R.methodsS3_1.8.2 cachem_1.0.6 polyclip_1.10-4 pkgload_1.3.2 [17] R.oo_1.25.0 ggforce_0.4.1 BiocManager_1.30.19 compiler_4.2.1 [21] Matrix_1.4-1 assertthat_0.2.1 fastmap_1.1.0 lazyeval_0.2.2 [25] cli_3.4.1 tweenr_2.0.2 later_1.3.0 htmltools_0.5.3 [29] tools_4.2.1 igraph_1.3.5 gtable_0.3.1 glue_1.6.2 [33] Rcpp_1.0.9 jquerylib_0.1.4 vctrs_0.5.1 nlme_3.1-157 [37] crosstalk_1.2.0 ggraph_2.1.0 paws.common_0.5.1 stringr_1.4.1 [41] ps_1.7.2 mime_0.12 lifecycle_1.0.3 renv_0.15.5 [45] MASS_7.3-57 scales_1.2.1 hms_1.1.2 promises_1.2.0.1 [49] rex_1.2.1 parallel_4.2.1 yaml_2.3.6 curl_4.3.3 [53] gridExtra_2.3 ggfun_0.0.9 yulab.utils_0.0.5 sass_0.4.2 [57] stringi_1.7.8 desc_1.4.2 cyclocomp_1.1.0 rlang_1.0.6 [61] pkgconfig_2.0.3 lattice_0.20-45 purrr_0.3.5 patchwork_1.1.2 [65] htmlwidgets_1.5.4 labeling_0.4.2 bit_4.0.5 tidyselect_1.2.0 [69] processx_3.8.0 magrittr_2.0.3 R6_2.5.1 generics_0.1.3 [73] pillar_1.8.1 withr_2.5.0 tibble_3.1.8 crayon_1.5.2 [77] utf8_1.2.2 viridis_0.6.2 grid_4.2.1 reactR_0.4.4 [81] blob_1.2.3 callr_3.7.3 digest_0.6.30 xtable_1.8-4 [85] R.cache_0.16.0 tidyr_1.2.1 httpuv_1.6.6 gridGraphics_0.5-1 [89] R.utils_2.12.2 munsell_0.5.0 viridisLite_0.4.1 ggplotify_0.1.0 [93] bslib_0.4.1
I didn't have rownames for the nodes table (format = tibble), which caused the error. It might be best to check that there are row numbers for the input nodes table.
Regardless of the layout that I set for
visIgraphLayout()
, I get the following error:It appears to be some issue with the graph structure that only comes into play when I use
visIgraphLayout()
withvisNetwork()
sessionInfo