Gets visNetwork graph with ppigraph, and optionally genes overview, metadata
get_visNetwork(ppigraph, genes_overview = NULL, sample_name = NULL)igraph object, get from get_ppigraph()
(optional) dataframe, default: NULL, else metadata dataframe for ppigraph proteins/genes aliases
(optional) character, default: NULL, else sample name found in genes_overview columns
list of visNetwork nodes and edges and given ppigraph
ppi_graph <- get_ppigraph(
get(load(system.file("extdata", "example_ppi_data.rda", package = "goatea")))
)
get_visNetwork(ppi_graph)
#> $nodes
#> label cluster degree betweenness closeness knn diversity id
#> 1 TP53 1 5 0 0.2 5 0.9979802 9606.ENSP00000269305
#> 2 EGFR 1 5 0 0.2 5 0.9958340 9606.ENSP00000275493
#> 3 SOX2 1 5 0 0.2 5 0.9021087 9606.ENSP00000323588
#> 4 MTOR 1 5 0 0.2 5 0.9300987 9606.ENSP00000354558
#> 5 BRCA1 1 5 0 0.2 5 0.9132782 9606.ENSP00000418960
#> 6 MYC 1 5 0 0.2 5 0.9916856 9606.ENSP00000478887
#> title color.background color.border
#> 1 Betweenness: 0 #E69F00FF #E69F00FF
#> 2 Betweenness: 0 #E69F00FF #E69F00FF
#> 3 Betweenness: 0 #E69F00FF #E69F00FF
#> 4 Betweenness: 0 #E69F00FF #E69F00FF
#> 5 Betweenness: 0 #E69F00FF #E69F00FF
#> 6 Betweenness: 0 #E69F00FF #E69F00FF
#>
#> $edges
#> combined_score from to edge_betweenness
#> 1 997 9606.ENSP00000269305 9606.ENSP00000478887 1
#> 2 999 9606.ENSP00000269305 9606.ENSP00000418960 1
#> 3 883 9606.ENSP00000269305 9606.ENSP00000323588 1
#> 4 874 9606.ENSP00000269305 9606.ENSP00000354558 1
#> 5 943 9606.ENSP00000269305 9606.ENSP00000275493 1
#> 6 802 9606.ENSP00000275493 9606.ENSP00000354558 1
#> 7 758 9606.ENSP00000275493 9606.ENSP00000323588 1
#> 8 800 9606.ENSP00000275493 9606.ENSP00000418960 1
#> 9 875 9606.ENSP00000275493 9606.ENSP00000478887 1
#> 10 958 9606.ENSP00000323588 9606.ENSP00000478887 1
#> 11 443 9606.ENSP00000323588 9606.ENSP00000418960 1
#> 12 419 9606.ENSP00000323588 9606.ENSP00000354558 1
#> 13 497 9606.ENSP00000354558 9606.ENSP00000418960 1
#> 14 730 9606.ENSP00000354558 9606.ENSP00000478887 1
#> 15 999 9606.ENSP00000418960 9606.ENSP00000478887 1
#> width id
#> 1 2.4931034 9606.ENSP00000269305_9606.ENSP00000478887
#> 2 2.5000000 9606.ENSP00000269305_9606.ENSP00000418960
#> 3 2.1000000 9606.ENSP00000269305_9606.ENSP00000323588
#> 4 2.0689655 9606.ENSP00000269305_9606.ENSP00000354558
#> 5 2.3068966 9606.ENSP00000269305_9606.ENSP00000275493
#> 6 1.8206897 9606.ENSP00000275493_9606.ENSP00000354558
#> 7 1.6689655 9606.ENSP00000275493_9606.ENSP00000323588
#> 8 1.8137931 9606.ENSP00000275493_9606.ENSP00000418960
#> 9 2.0724138 9606.ENSP00000275493_9606.ENSP00000478887
#> 10 2.3586207 9606.ENSP00000323588_9606.ENSP00000478887
#> 11 0.5827586 9606.ENSP00000323588_9606.ENSP00000418960
#> 12 0.5000000 9606.ENSP00000323588_9606.ENSP00000354558
#> 13 0.7689655 9606.ENSP00000354558_9606.ENSP00000418960
#> 14 1.5724138 9606.ENSP00000354558_9606.ENSP00000478887
#> 15 2.5000000 9606.ENSP00000418960_9606.ENSP00000478887
#> title
#> 1 STRING score: 997<br>Betweenness: 1<br>
#> 2 STRING score: 999<br>Betweenness: 1<br>
#> 3 STRING score: 883<br>Betweenness: 1<br>
#> 4 STRING score: 874<br>Betweenness: 1<br>
#> 5 STRING score: 943<br>Betweenness: 1<br>
#> 6 STRING score: 802<br>Betweenness: 1<br>
#> 7 STRING score: 758<br>Betweenness: 1<br>
#> 8 STRING score: 800<br>Betweenness: 1<br>
#> 9 STRING score: 875<br>Betweenness: 1<br>
#> 10 STRING score: 958<br>Betweenness: 1<br>
#> 11 STRING score: 443<br>Betweenness: 1<br>
#> 12 STRING score: 419<br>Betweenness: 1<br>
#> 13 STRING score: 497<br>Betweenness: 1<br>
#> 14 STRING score: 730<br>Betweenness: 1<br>
#> 15 STRING score: 999<br>Betweenness: 1<br>
#>
#> $ppigraph
#> IGRAPH b56a099 UNW- 6 15 --
#> + attr: central gene (g/c), modularity (g/n), transitivity (g/n),
#> | assortattivity (g/n), mean distance (g/n), edge density (g/n), degree
#> | centralization (g/n), betweenness centralization (g/n), closeness
#> | centralization (g/n), eigen centralization (g/n), name (v/c), cluster
#> | (v/n), degree (v/n), betweenness (v/n), closeness (v/n), knn (v/n),
#> | diversity (v/n), id (v/c), combined_score (e/n), from (e/c), to
#> | (e/c), edge_betweenness (e/n), weight (e/n)
#> + edges from b56a099 (vertex names):
#> [1] TP53--MYC TP53--BRCA1 TP53--SOX2 TP53--MTOR TP53--EGFR EGFR--MTOR
#> [7] EGFR--SOX2 EGFR--BRCA1 EGFR--MYC SOX2--MYC SOX2--BRCA1 SOX2--MTOR
#> + ... omitted several edges
#>