11 Perform each process separately

The same process as functions like refseq can be performed separately. This is useful for piped processing and for individual customization in each process.

library(biotextgraph)
btg <- obtain_refseq(c("DDX41","PNKP","IRF3")) |>
  set_filter_words() |>
  make_corpus() |>
  make_TDM() |>
  make_graph() |>
  graph_cluster() |>
  process_network_gene(gene_plot=TRUE, gene_path_plot="reactome") |>
  plot_biotextgraph(edge_link=FALSE) |>
  plot_wordcloud()
#> Input genes: 3
#>   Converted input genes: 3
#> Filter based on GeneSummary
#> Filtered 76 words (frequency and/or tfidf)
#> Found 21 enriched term
btg
#> Type: refseq
#> Number of words: 30
#> Query: DDX41/PNKP/IRF3
#> Graph: V(33), E(471)
#> Degree: response(32)/DNA(31)/immune(31)/innate(31)/phosphorylation(31)
#> 313 Kb

## Text of enrichment analysis results
btg2 <- obtain_enrich(c("DDX41","PNKP","IRF3"), enrich="reactome") |>
  set_filter_words() |>
  make_corpus() |>
  make_TDM() |>
  make_graph() |>
  process_network_manual() |>
  plot_biotextgraph(edge_link=FALSE)
#> Input genes: 3
#>   Converted input genes: 3
#> Performing enrichment analysis
#> Filter based on GeneSummary
#> Filtered 76 words (frequency and/or tfidf)
btg2
#> Type: enrich
#> Number of words: 30
#> Query: DDX41/PNKP/IRF3
#> Graph: V(29), E(40)
#> Degree: immune(7)/innate(7)/responses(7)/activatesmodulates(5)/adaptive(4)
#> 303.5 Kb

11.1 Use of gene descriptions in Alliance of Genome Resources

We can use gene descriptions of alliance of genome resources, that can be obtained from here. Download the file and call obtain_alliance function. The default path is set to the working directory and human gene description.

btg_agr <- obtain_alliance(c("DDX41","PNKP","IRF3")) |>
  make_corpus() |> ## No filter this time
  make_TDM() |>
  make_graph() |>
  graph_cluster() |>
  process_network_gene(gene_plot=TRUE, gene_path_plot="reactome") |>
  plot_biotextgraph(edge_link=FALSE)
#> Input genes: 3
#> Found 21 enriched term

10 Parsing