inject linefeeds for node names for graph, with textual annotation from ontology

Usage

improve_nodes(g, ont)

Arguments

g: graphNEL instance
ont: instance of ontology from ontologyIndex

Value

graphNEL instance

Examples

requireNamespace("Rgraphviz")
requireNamespace("graph")
clcon <- retrieve_semsql_conn("cl")
cl <- semsql_to_oi(clcon)
#> Warning: Some parent terms not found: BFO:0000002, BFO:0000004, SO:0000704 (15 more)
cl3k <- c(
  "CL:0000492", "CL:0001054", "CL:0000236", "CL:0000625",
  "CL:0000576", "CL:0000623", "CL:0000451", "CL:0000556"
)
p3k <- ontologyPlot::onto_plot(cl, cl3k)
gnel <- make_graphNEL_from_ontology_plot(p3k)
head(graph::nodes(gnel)) # before improving
#> [1] "CL:0000255" "CL:0000988" "CL:0000842" "CL:0000542" "CL:0000791"
#> [6] "CL:0000492"
gnel <- improve_nodes(gnel, cl)
head(graph::nodes(gnel))
#> [1] "eukaryotic\ncell\nCL:0000255"           
#> [2] "hematopoietic\ncell\nCL:0000988"        
#> [3] "mononuclear\nleukocyte\nCL:0000842"     
#> [4] "lymphocyte\nCL:0000542"                 
#> [5] "mature\nalpha-beta T cell\nCL:0000791"  
#> [6] "CD4-positive\nhelper T cell\nCL:0000492"