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) (2024-01-23 r85822)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.3 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
##
## 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_0.99.0
##
## loaded via a namespace (and not attached):
## [1] grr_0.9.5 rlang_1.1.3
## [3] magrittr_2.0.3 clue_0.3-65
## [5] GetoptLong_1.0.5 matrixStats_1.2.0
## [7] compiler_4.4.0 png_0.1-8
## [9] systemfonts_1.0.5 vctrs_0.6.5
## [11] maps_3.4.2 gprofiler2_0.2.2
## [13] rvest_1.0.3 stringr_1.5.1
## [15] shape_1.4.6 pkgconfig_2.0.3
## [17] crayon_1.5.2 fastmap_1.1.1
## [19] ellipsis_0.3.2 backports_1.4.1
## [21] utf8_1.2.4 promises_1.2.1
## [23] rmarkdown_2.25 ragg_1.2.7
## [25] purrr_1.0.2 xfun_0.41
## [27] cachem_1.0.8 pals_1.9
## [29] aplot_0.2.2 jsonlite_1.8.8
## [31] progress_1.2.3 later_1.3.2
## [33] cluster_2.1.6 broom_1.0.5
## [35] parallel_4.4.0 prettyunits_1.2.0
## [37] R6_2.5.1 rols_2.31.0
## [39] RColorBrewer_1.1-3 bslib_0.6.1
## [41] stringi_1.8.3 car_3.1-2
## [43] jquerylib_0.1.4 Rcpp_1.0.12
## [45] iterators_1.0.14 knitr_1.45
## [47] IRanges_2.37.1 httpuv_1.6.14
## [49] igraph_2.0.1.1 Matrix_1.6-5
## [51] tidyselect_1.2.0 dichromat_2.0-0.1
## [53] abind_1.4-5 yaml_2.3.8
## [55] doParallel_1.0.17 codetools_0.2-19
## [57] lattice_0.22-5 tibble_3.2.1
## [59] shiny_1.8.0 Biobase_2.63.0
## [61] treeio_1.27.0 evaluate_0.23
## [63] gridGraphics_0.5-1 desc_1.4.3
## [65] xml2_1.3.6 circlize_0.4.15
## [67] pillar_1.9.0 ggtree_3.11.0
## [69] ggpubr_0.6.0 carData_3.0-5
## [71] stats4_4.4.0 foreach_1.5.2
## [73] ggfun_0.1.4 plotly_4.10.4
## [75] generics_0.1.3 S4Vectors_0.41.3
## [77] hms_1.1.3 ggplot2_3.4.4
## [79] munsell_0.5.0 scales_1.3.0
## [81] tidytree_0.4.6 xtable_1.8-4
## [83] glue_1.7.0 orthogene_1.9.0
## [85] mapproj_1.2.11 scatterplot3d_0.3-44
## [87] lazyeval_0.2.2 tools_4.4.0
## [89] data.table_1.15.0 ggsignif_0.6.4
## [91] babelgene_22.9 fs_1.6.3
## [93] tidygraph_1.3.1 grid_4.4.0
## [95] tidyr_1.3.1 ape_5.7-1
## [97] colorspace_2.1-0 nlme_3.1-164
## [99] patchwork_1.2.0 homologene_1.4.68.19.3.27
## [101] cli_3.6.2 Polychrome_1.5.1
## [103] textshaping_0.3.7 fansi_1.0.6
## [105] viridisLite_0.4.2 ComplexHeatmap_2.19.0
## [107] dplyr_1.1.4 gtable_0.3.4
## [109] rstatix_0.7.2 yulab.utils_0.1.4
## [111] sass_0.4.8 digest_0.6.34
## [113] BiocGenerics_0.49.1 ggplotify_0.1.2
## [115] rjson_0.2.21 htmlwidgets_1.6.4
## [117] memoise_2.0.1 htmltools_0.5.7
## [119] pkgdown_2.0.7 simona_1.1.6
## [121] lifecycle_1.0.4 httr_1.4.7
## [123] mime_0.12 GlobalOptions_0.1.2