Seems to only be for certain cell types, eg.
ggnetwork_plot_full
Subsetting results by phenotype.
get_cell_ontology
Importing existing file: /Users/schilder/Library/Caches/org.R-project.R/R/HPOExplorer/data/phenotype_to_genes.txt
5 associations remain after filtering.
Creating adjacency matrix for 5 terms.
Making hoverboxes from: 'Phenotype', 'HPO_ID', 'description', 'CellType', 'p', 'q', 'fold_change'
Making phenotype network object.
Getting ontology level for 5 HPO IDs.
Creating ggnetwork plot.
Error in cbind(x, y, others) : object 'x' not found
Error in cbind(x, y, others) : object 'x' not found
14.
cbind(x, y, others)
13.
rbind(cbind(x, y, others), cbind(x = xend, y = yend, others))
12.
eval(substitute(expr), data, enclos = parent.frame())
11.
eval(substitute(expr), data, enclos = parent.frame())
10.
with.default(data, {
rbind(cbind(x, y, others), cbind(x = xend, y = yend, others))
})
9.
with(data, {
rbind(cbind(x, y, others), cbind(x = xend, y = yend, others))
})
8.
to_basic.GeomSegment(data[[i]], prestats_data[[i]], layout, params[[i]],
p)
7.
to_basic(data[[i]], prestats_data[[i]], layout, params[[i]],
p)
6.
layers2traces(data, prestats_data, layout, plot)
5.
gg2list(p, width = width, height = height, tooltip = tooltip,
dynamicTicks = dynamicTicks, layerData = layerData, originalData = originalData,
source = source, ...)
4.
ggplotly.ggplot(p = network_plot, tooltip = tooltip)
3.
plotly::ggplotly(p = network_plot, tooltip = tooltip) at ggnetwork_plot.R#61
2.
plotly::layout(plotly::ggplotly(p = network_plot, tooltip = tooltip),
hoverlabel = list(align = "left")) at ggnetwork_plot.R#61
1.
HPOExplorer::ggnetwork_plot(phenoNet = phenoNet, colour_var = colour_var,
interactive = interactive, verbose = verbose)
```
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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 utils datasets methods base
other attached packages:
[1] MultiEWCE_0.1.2
loaded via a namespace (and not attached):
[1] backports_1.4.1 AnnotationHub_3.6.0 BiocFileCache_2.6.0
[4] plyr_1.8.8 lazyeval_0.2.2 orthogene_1.4.1
[7] ewceData_1.6.0 BiocParallel_1.32.5 GenomeInfoDb_1.34.6
[10] ggnetwork_0.5.10 ggplot2_3.4.0 digest_0.6.31
[13] yulab.utils_0.0.6 ensembldb_2.22.0 htmltools_0.5.4
[16] RNOmni_1.0.1 fansi_1.0.3 magrittr_2.0.3
[19] memoise_2.0.1 ontologyPlot_1.6 limma_3.54.0
[22] sna_2.7 Biostrings_2.66.0 matrixStats_0.63.0
[25] R.utils_2.12.2 prettyunits_1.1.1 colorspace_2.0-3
[28] blob_1.2.3 rappdirs_0.3.3 xfun_0.36
[31] dplyr_1.0.10 crayon_1.5.2 RCurl_1.98-1.9
[34] jsonlite_1.8.4 graph_1.76.0 templateR_0.99.0
[37] ape_5.6-2 glue_1.6.2 gtable_0.3.1
[40] zlibbioc_1.44.0 XVector_0.38.0 HGNChelper_0.8.1
[43] DelayedArray_0.24.0 car_3.1-1 Rgraphviz_2.42.0
[46] SingleCellExperiment_1.20.0 BiocGenerics_0.44.0 abind_1.4-5
[49] scales_1.2.1 DBI_1.1.3 rstatix_0.7.1
[52] Rcpp_1.0.9 progress_1.2.2 viridisLite_0.4.1
[55] xtable_1.8-4 gridGraphics_0.5-1 tidytree_0.4.2
[58] bit_4.0.5 DT_0.27 stats4_4.2.1
[61] htmlwidgets_1.6.1 httr_1.4.4 ontologyIndex_2.10
[64] HPOExplorer_0.99.2 ellipsis_0.3.2 farver_2.1.1
[67] pkgconfig_2.0.3 XML_3.99-0.13 R.methodsS3_1.8.2
[70] dbplyr_2.3.0 utf8_1.2.2 labeling_0.4.2
[73] ggplotify_0.1.0 tidyselect_1.2.0 rlang_1.0.6
[76] reshape2_1.4.4 later_1.3.0 AnnotationDbi_1.60.0
[79] munsell_0.5.0 BiocVersion_3.16.0 tools_4.2.1
[82] cachem_1.0.6 cli_3.6.0 generics_0.1.3
[85] RSQLite_2.2.20 ExperimentHub_2.6.0 statnet.common_4.7.0
[88] broom_1.0.2 evaluate_0.20 stringr_1.5.0
[91] fastmap_1.1.0 EnsDb.Hsapiens.v75_2.99.0 yaml_2.3.6
[94] ggtree_3.6.2 knitr_1.41 babelgene_22.9
[97] bit64_4.0.5 purrr_1.0.1 AnnotationFilter_1.22.0
[100] KEGGREST_1.38.0 gprofiler2_0.2.1 nlme_3.1-161
[103] mime_0.12 R.oo_1.25.0 grr_0.9.5
[106] aplot_0.1.9 xml2_1.3.3 biomaRt_2.54.0
[109] brio_1.1.3 compiler_4.2.1 rstudioapi_0.14
[112] plotly_4.10.1 filelock_1.0.2 curl_5.0.0
[115] png_0.1-8 interactiveDisplayBase_1.36.0 testthat_3.1.6
[118] ggsignif_0.6.4 treeio_1.22.0 paintmap_1.0
[121] tibble_3.1.8 EWCE_1.6.0 homologene_1.4.68.19.3.27
[124] stringi_1.7.12 desc_1.4.2 GenomicFeatures_1.50.3
[127] lattice_0.20-45 ProtGenerics_1.30.0 Matrix_1.5-3
[130] vctrs_0.5.1 pillar_1.8.1 lifecycle_1.0.3
[133] BiocManager_1.30.19 data.table_1.14.6 bitops_1.0-7
[136] httpuv_1.6.8 patchwork_1.1.2 rtracklayer_1.58.0
[139] GenomicRanges_1.50.2 BiocIO_1.8.0 R6_2.5.1
[142] promises_1.2.0.1 network_1.18.0 IRanges_2.32.0
[145] codetools_0.2-18 pkgload_1.3.2 assertthat_0.2.1
[148] SummarizedExperiment_1.28.0 rprojroot_2.0.3 rjson_0.2.21
[151] GenomicAlignments_1.34.0 Rsamtools_2.14.0 S4Vectors_0.36.1
[154] GenomeInfoDbData_1.2.9 hms_1.1.2 parallel_4.2.1
[157] grid_4.2.1 ggfun_0.0.9 waldo_0.4.0
[160] tidyr_1.2.1 coda_0.19-4 rmarkdown_2.19
[163] MatrixGenerics_1.10.0 carData_3.0-5 ggpubr_0.5.0
[166] piggyback_0.1.4 Biobase_2.58.0 shiny_1.7.4
[169] restfulr_0.0.15