:::
r onc_enrich_report[['config']][['ppi']][['string']][['network_type']]
network_type
parameter in the STRING APIr onc_enrich_report[['config']][['ppi']][['string']][['add_nodes']]
proteins that interact with proteins in the query setadd_nodes
parameter in the STRING APIr onc_enrich_report[['config']][['ppi']][['string']][['minimum_score']]
(range 0-1)required_score
parameter in the STRING APIr onc_enrich_report[['config']][['ppi']][['string']][['show_drugs']]
r onc_enrich_report[['config']][['ppi']][['string']][['show_isolated_nodes']]
visNetwork::visNetwork( onc_enrich_report[['data']][['ppi']][['string']][['complete_network']]$nodes, onc_enrich_report[['data']][['ppi']][['string']][['complete_network']]$edges) |> visNetwork::visInteraction(multiselect = TRUE, tooltipDelay = 300) |> visNetwork::visIgraphLayout(layout="layout_nicely")
cat('<br>') cat('\n <ul><li> <i> <span style="font-size: 100%; padding: 3px; background-color:#989898; color:white"> No protein-protein interactions from STRING were found among members in the query set (with the required association score). Lowering the assocation score threshold of for interactions in STRING may provide a network. </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
visNetwork::visNetwork( onc_enrich_report[['data']][['ppi']][['string']][['community_network']]$nodes, onc_enrich_report[['data']][['ppi']][['string']][['community_network']]$edges) |> visNetwork::visInteraction(multiselect = TRUE, tooltipDelay = 300) |> visNetwork::visIgraphLayout(layout="layout_nicely")
cat('<br>') cat('\n <ul><li> <i> <span style="font-size: 100%; padding: 3px; background-color:#989898; color:white"> No network communities were found among members in the query set (with the required association score). Lowering the assocation score threshold of for interactions in STRING may provide a network and associated communities. </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
htmltools::br() DT::datatable(onc_enrich_report[['data']][['ppi']][['string']][['hubscores']], escape = F, extensions=c("Buttons","Responsive"), width = "100%", options=list(buttons = c('csv','excel'),dom = 'Bfrtip', pagelength = 20)) |> DT::formatStyle("symbol","hub_score", color = "white", backgroundColor = DT::styleInterval(onc_enrich_report[['config']][['disease']][['breaks']], onc_enrich_report[['config']][['disease']][['colors']]))
cat('<br>') cat('\n <ul><li> <i> <span style="font-size: 100%; padding: 3px; background-color:#989898; color:white"> No hubscores from the protein-protein interaction network were established for members in the query set (with the required association score). Lowering the assocation score threshold of for interactions in STRING may provide a network with hubscores. </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
r onc_enrich_report[['config']][['ppi']][['biogrid']][['add_nodes']]
targets that are not part of the query set, but that interact with members of the query setr onc_enrich_report[['config']][['ppi']][['biogrid']][['minimum_evidence']]
r onc_enrich_report[['config']][['ppi']][['biogrid']][['show_drugs']]
r onc_enrich_report[['config']][['ppi']][['biogrid']][['show_isolated_nodes']]
visNetwork::visNetwork( onc_enrich_report[['data']][['ppi']][['biogrid']][['complete_network']]$nodes, onc_enrich_report[['data']][['ppi']][['biogrid']][['complete_network']]$edges) |> visNetwork::visInteraction(multiselect = TRUE, tooltipDelay = 300) |> visNetwork::visIgraphLayout(layout="layout_nicely")
cat('<br>') cat('\n <ul><li> <i> <span style="font-size: 100%; padding: 3px; background-color:#989898; color:white"> No protein-protein interactions from BioGRID were found among members in the query set (with the required evidence support). Lowering the required evidence support for interactions in BioGRID may provide a network. </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
visNetwork::visNetwork( onc_enrich_report[['data']][['ppi']][['biogrid']][['community_network']]$nodes, onc_enrich_report[['data']][['ppi']][['biogrid']][['community_network']]$edges) |> visNetwork::visInteraction(multiselect = TRUE, tooltipDelay = 300) |> visNetwork::visIgraphLayout(layout="layout_nicely")
cat('<br>') cat('\n <ul><li> <i> <span style="font-size: 100%; padding: 3px; background-color:#989898; color:white"> No network communities were found among members in the query set (with the required evidence support). Lowering the required evidence support for interactions in BioGRID may provide a network and associated communities. </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
htmltools::br() DT::datatable(onc_enrich_report[['data']][['ppi']][['biogrid']][['hubscores']], escape = F, extensions=c("Buttons","Responsive"), width = "100%", options=list(buttons = c('csv','excel'),dom = 'Bfrtip', pagelength = 20)) |> DT::formatStyle("symbol","hub_score", color = "white", backgroundColor = DT::styleInterval( onc_enrich_report[['config']][['disease']][['breaks']], onc_enrich_report[['config']][['disease']][['colors']]) )
cat('<br>') cat('\n <ul><li> <i> <span style="font-size: 100%; padding: 3px; background-color:#989898; color:white"> No hubscores from the protein-protein interaction network were established for members in the query set (with the required evidence support). Lowering the required evidence support for interactions in BioGRID may provide a network with hubscores. </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
Citation Note : If you use the output of the Protein-protein interaction network module of oncoEnrichR in your research, please cite the following resources and tools as appropriate:
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