vignettes/KGExplorer.Rmd
KGExplorer.Rmd
g <- get_monarch_kg()
g2 <- filter_kg(g,
to_categories = c("biolink:Disease",
"biolink:PhenotypicFeature"),
from_categories = "biolink:Cell")
plot_graph_visnetwork(g2,
selectedBy = "id",
label_var = "name",
layout = "layout_nicely",
colour_var = "category")
dat <- map_upheno_data()
upheno_plots <- plot_upheno(dat)
gm <- link_monarch(maps = list(
c("variant","disease"),
c("variant","phenotype"),
c("variant","gene")
))
gm2 <- tidygraph::graph_join(gm,g)
gm2 <- filter_graph(gm2,
node_filters = list(category=c("disease",
"phenotype",
"phenotypicfeature",
"gene","variant")))
gm3 <- filter_graph(g = gm2,
size=20000)
igraph::vertex_attr(gm3,"category") <-
tolower(gsub("biolink:","",igraph::vertex_attr(gm3,"category")))
igraph::vertex_attr(gm3,"name") <- igraph::vertex_attr(gm3,"id")
plot_graph_visnetwork(gm3,
selectedBy = "category",
label_var = "name",
layout = "layout_nicely",
colour_var = "category")
utils::sessionInfo()## R Under development (unstable) (2024-12-15 r87442)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] KGExplorer_0.99.05
##
## loaded via a namespace (and not attached):
## [1] grr_0.9.5 httr2_1.0.7
## [3] rlang_1.1.4 magrittr_2.0.3
## [5] clue_0.3-66 GetoptLong_1.0.5
## [7] matrixStats_1.4.1 compiler_4.5.0
## [9] png_0.1-8 systemfonts_1.1.0
## [11] vctrs_0.6.5 maps_3.4.2.1
## [13] gprofiler2_0.2.3 stringr_1.5.1
## [15] rvest_1.0.4 shape_1.4.6.1
## [17] pkgconfig_2.0.3 crayon_1.5.3
## [19] fastmap_1.2.0 backports_1.5.0
## [21] promises_1.3.2 rmarkdown_2.29
## [23] ragg_1.3.3 purrr_1.0.2
## [25] xfun_0.49 cachem_1.1.0
## [27] pals_1.9 aplot_0.2.4
## [29] jsonlite_1.8.9 later_1.4.1
## [31] BiocParallel_1.41.0 cluster_2.1.8
## [33] broom_1.0.7 parallel_4.5.0
## [35] R6_2.5.1 rols_3.3.0
## [37] stringi_1.8.4 RColorBrewer_1.1-3
## [39] bslib_0.8.0 car_3.1-3
## [41] jquerylib_0.1.4 Rcpp_1.0.13-1
## [43] iterators_1.0.14 knitr_1.49
## [45] IRanges_2.41.2 httpuv_1.6.15
## [47] igraph_2.1.2 Matrix_1.7-1
## [49] tidyselect_1.2.1 dichromat_2.0-0.1
## [51] abind_1.4-8 yaml_2.3.10
## [53] doParallel_1.0.17 codetools_0.2-20
## [55] lattice_0.22-6 tibble_3.2.1
## [57] shiny_1.10.0 Biobase_2.67.0
## [59] treeio_1.31.0 evaluate_1.0.1
## [61] gridGraphics_0.5-1 desc_1.4.3
## [63] xml2_1.3.6 circlize_0.4.16
## [65] pillar_1.10.0 ggtree_3.15.0
## [67] ggpubr_0.6.0 carData_3.0-5
## [69] stats4_4.5.0 foreach_1.5.2
## [71] ggfun_0.1.8 plotly_4.10.4
## [73] generics_0.1.3 S4Vectors_0.45.2
## [75] ggplot2_3.5.1 munsell_0.5.1
## [77] scales_1.3.0 tidytree_0.4.6
## [79] xtable_1.8-4 glue_1.8.0
## [81] orthogene_1.13.0 mapproj_1.2.11
## [83] scatterplot3d_0.3-44 lazyeval_0.2.2
## [85] tools_4.5.0 data.table_1.16.4
## [87] ggsignif_0.6.4 babelgene_22.9
## [89] fs_1.6.5 tidygraph_1.3.1
## [91] grid_4.5.0 tidyr_1.3.1
## [93] ape_5.8-1 colorspace_2.1-1
## [95] nlme_3.1-166 patchwork_1.3.0
## [97] homologene_1.4.68.19.3.27 Formula_1.2-5
## [99] cli_3.6.3 rappdirs_0.3.3
## [101] Polychrome_1.5.1 textshaping_0.4.1
## [103] viridisLite_0.4.2 ComplexHeatmap_2.23.0
## [105] dplyr_1.1.4 gtable_0.3.6
## [107] rstatix_0.7.2 yulab.utils_0.1.8
## [109] sass_0.4.9 digest_0.6.37
## [111] BiocGenerics_0.53.3 ggplotify_0.1.2
## [113] rjson_0.2.23 htmlwidgets_1.6.4
## [115] farver_2.1.2 htmltools_0.5.8.1
## [117] pkgdown_2.1.1 simona_1.5.0
## [119] lifecycle_1.0.4 httr_1.4.7
## [121] mime_0.12 GlobalOptions_0.1.2