1) Secreted Signaling (Paracrine/autocrine signaling) 2) ECM-Receptor (extracellular matrix-receptor interactions) 3) Cell-Cell Contact
active_tab <- list() for(cl in c('ss','ecm','ccc')){ active_tab[[cl]] <- F } if(NROW(onc_enrich_report[['data']][['ligand_receptor']][['secreted_signaling']]) > 0){ active_tab[['ss']] <- T }else{ if(NROW(onc_enrich_report[['data']][['ligand_receptor']][['ecm_receptor']]) > 0){ active_tab[['ecm']] <- T }else{ if(NROW(onc_enrich_report[['data']][['ligand_receptor']][['cell_cell_contact']]) > 0){ active_tab[['ccc']] <- T } } } if(active_tab[['ss']] == F & active_tab[['ecm']] == F & active_tab[['ccc']] == F){ active_tab[['ss']] <- T }
if(active_tab[['ss']] == T){ cat("") cat("#### Secreted Signaling {.active}") cat("") }else{ cat("") cat("#### Secreted Signaling") cat("") }
ligand_interactions_ss <- crosstalk::SharedData$new(onc_enrich_report[['data']][['ligand_receptor']][['secreted_signaling']]) crosstalk::bscols( list( crosstalk::filter_select("ligand", "Ligand", ligand_interactions_ss, ~ligand) ), list( crosstalk::filter_select("receptor", "Receptor", ligand_interactions_ss, ~receptor) ) ) htmltools::br() DT::datatable( ligand_interactions_ss, escape = F, extensions=c("Buttons","Responsive"), width = "100%", style = 'bootstrap', rownames = F, options=list(buttons = c('csv','excel'), pageLength = 10, bPaginate = T, dom = 'Bfrtip') )
cat('\n <ul><li> <i> <span style="font-size: 105%; padding: 3px; background-color:#989898; color:white"> <b>NO</b> pair of genes in the queryset are involved in ligand-receptor interactions (<b>CellChatDB - Secreted signalling</b>) </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
if(active_tab[['ecm']] == T){ cat("") cat("#### ECM-Receptor {.active}") cat("") }else{ cat("") cat("#### ECM-Receptor") cat("") }
ligand_interactions_ecm <- crosstalk::SharedData$new(onc_enrich_report[['data']][['ligand_receptor']][['ecm_receptor']]) crosstalk::bscols( list( crosstalk::filter_select("ligand", "Ligand", ligand_interactions_ecm, ~ligand) ), list( crosstalk::filter_select("receptor", "Receptor", ligand_interactions_ecm, ~receptor) ) ) htmltools::br() DT::datatable( ligand_interactions_ecm, escape = F, extensions=c("Buttons","Responsive"), width = "100%", style = 'bootstrap', rownames = F, options=list(buttons = c('csv','excel'), pageLength = 10, bPaginate = T, dom = 'Bfrtip') )
cat('\n <ul><li> <i> <span style="font-size: 105%; padding: 3px; background-color:#989898; color:white"> <b>NO</b> pair of genes in the queryset are involved in ligand-receptor interactions (<b>CellChatDB - ECM Receptor</b>) </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
if(active_tab[['ccc']] == T){ cat("") cat("#### Cell-Cell Contact {.active}") cat("") }else{ cat("") cat("#### Cell-Cell Contact") cat("") }
ligand_interactions_ccc <- crosstalk::SharedData$new(onc_enrich_report[['data']][['ligand_receptor']][['cell_cell_contact']]) crosstalk::bscols( list( crosstalk::filter_select("ligand", "Ligand", ligand_interactions_ccc, ~ligand) ), list( crosstalk::filter_select("receptor", "Receptor", ligand_interactions_ccc, ~receptor) ) ) htmltools::br() DT::datatable( ligand_interactions_ccc, escape = F, extensions=c("Buttons","Responsive"), width = "100%", style = 'bootstrap', rownames = F, options=list(buttons = c('csv','excel'), pageLength = 10, bPaginate = T, dom = 'Bfrtip') )
cat('\n <ul><li> <i> <span style="font-size: 105%; padding: 3px; background-color:#989898; color:white"> <b>NO</b> pair of genes in the queryset are involved in ligand-receptor interactions (<b>CellChatDB - Cell-Cell Contact</b>) </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
Citation Note : If you use the output of the Ligand-receptor interactions module of oncoEnrichR in your research, please cite the following resources and tools as appropriate:
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