show_tcga_coexp <- list() coexp_data <- list() active_tab <- list() for(n in c('Positive','Negative')){ show_tcga_coexp[[n]] <- TRUE coexp_data[[n]] <- data.frame() active_tab[[n]] <- FALSE coexp_data[[n]] <- onc_enrich_report[['data']][['tcga']][['coexpression']] |> dplyr::filter(corrtype == n) |> dplyr::select(-corrtype) |> head(2500) if(n == 'Negative'){ coexp_data[[n]] <- coexp_data[[n]] |> dplyr::arrange(r) } if(nrow(coexp_data[[n]]) == 0){ show_tcga_coexp[[n]] <- FALSE } } if(show_tcga_coexp[['Positive']] == T){ active_tab[['Positive']] <- T }else{ if(show_tcga_coexp[['Negative']] == T){ active_tab[['Negative']] <- T }else{ active_tab[['Positive']] <- T } }
if(active_tab[['Positive']] == T){ cat("") cat("#### Positive correlation {.active}") cat("") }else{ cat("") cat("#### Positive correlation") cat("") }
coexp_genes_positive <- crosstalk::SharedData$new(coexp_data[['Positive']]) crosstalk::bscols( list( crosstalk::filter_select("target_gene", "Target gene", coexp_genes_positive, ~target_gene), crosstalk::filter_slider("r", "Correlation coefficient (r)", coexp_genes_positive, ~r, step = 0.05, min = 0.7, max = 1), crosstalk::filter_checkbox("tumor_suppressor", "Tumor suppressor (partner)", coexp_genes_positive, ~tumor_suppressor) ), list( crosstalk::filter_checkbox("oncogene", "Proto-oncogene (partner)", coexp_genes_positive, ~oncogene), crosstalk::filter_checkbox("cancer_driver", "Cancer driver (partner)", coexp_genes_positive, ~cancer_driver), crosstalk::filter_select("primary_site", "Primary site", coexp_genes_positive, ~primary_site) ) ) htmltools::br() DT::datatable(coexp_genes_positive, escape = F, extensions=c("Buttons","Responsive"), width = "100%", options=list(buttons = c('csv','excel'),dom = 'Bfrtip') ) rm(coexp_genes_positive)
cat('<br><br>\n <ul><li> <i> <span style="font-size: 105%; padding: 3px; background-color:#989898; color:white"> No genes in the query set with strong positive correlations to tumor suppressors, oncogenes or cancer drivers. </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
if(active_tab[['Negative']] == T){ cat("") cat("#### Negative correlation {.active}") cat("") }else{ cat("") cat("#### Negative correlation") cat("") }
coexp_genes_negative <- crosstalk::SharedData$new(coexp_data[['Negative']]) crosstalk::bscols( list( crosstalk::filter_select("target_gene", "Target gene", coexp_genes_negative,~target_gene), crosstalk::filter_slider("r", "Correlation coefficient (r)", coexp_genes_negative, ~r, step = 0.05, min = -1, max = -0.7), crosstalk::filter_checkbox("tumor_suppressor", "Tumor suppressor (partner)", coexp_genes_negative, ~tumor_suppressor) ), list( crosstalk::filter_checkbox("oncogene", "Proto-oncogene (partner)", coexp_genes_negative, ~oncogene), crosstalk::filter_checkbox("cancer_driver", "Cancer driver (partner)", coexp_genes_negative, ~cancer_driver), crosstalk::filter_select("primary_site", "Primary site", coexp_genes_negative, ~primary_site) ) ) htmltools::br() DT::datatable(coexp_genes_negative, escape = F, extensions=c("Buttons","Responsive"), width = "100%", options=list(buttons = c('csv','excel'),dom = 'Bfrtip') ) rm(coexp_genes_negative) rm(coexp_data)
cat('<br><br>\n <ul><li> <i> <span style="font-size: 105%; padding: 3px; background-color:#989898; color:white"> No genes in the query set with strong negative correlations to tumor suppressors, oncogenes or cancer drivers. </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
Citation Note : If you use the output of the Tumor co-expression module of oncoEnrichR in your research, please cite the following resources and tools:
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