Size of gene paralog family
The higher the prediction score, the more confident the prediction is with respect to a synthetic lethality interaction. Interactions are here ranked according to confidence (percentile), visualized in varying shades of blue (from low-confident interactions to high-confident interactions ).
sl_interactions <- list() sl_interactions[['a_b']] <- data.frame() sl_interactions[['a_only']] <- data.frame() active_tab <- list() active_tab[['a_b']] <- F active_tab[['a_only']] <- F if(NROW(onc_enrich_report[['data']][['synleth']][['both_in_pair']]) > 0){ sl_interactions[['a_b']] <- onc_enrich_report[['data']][['synleth']][['both_in_pair']] |> dplyr::filter(.data$prediction_percentile < 50) |> head(2500) active_tab[['a_b']] <- T } if(NROW(onc_enrich_report[['data']][['synleth']][['single_pair_member']]) > 0){ sl_interactions[['a_only']] <- onc_enrich_report[['data']][['synleth']][['single_pair_member']] |> dplyr::filter(.data$prediction_percentile < 50) |> head(2500) if(active_tab[['a_b']] == F){ active_tab[['a_only']] <- T } }
if(active_tab[['a_b']] == T){ cat("") cat("##### Both pair members in query set {.active}") cat("") }else{ cat("") cat("##### Both pair members in query set") cat("") }
sl_ab <- crosstalk::SharedData$new(sl_interactions[['a_b']]) crosstalk::bscols( list( crosstalk::filter_select("gene_A", "Interactor A", sl_ab, ~gene_A), crosstalk::filter_select("gene_B", "Interactor B", sl_ab, ~gene_B), crosstalk::filter_slider("prediction_score", "Prediction score", sl_ab, ~prediction_score, step = 0.025, min = 0.0, max = 0.45), crosstalk::filter_slider("prediction_percentile", "Prediction percentile", sl_ab, ~prediction_percentile, min = 0.0, step = 2, max = 50) ), list( crosstalk::filter_slider("sequence_identity_pct", "Sequence identity (percent)", sl_ab, ~sequence_identity_pct, min = 0, max = 100), crosstalk::filter_slider("family_size", "Gene family size", sl_ab, ~family_size) ) ) htmltools::br() DT::datatable( sl_ab, escape = F, extensions=c("Buttons","Responsive"), width = "100%", style = 'bootstrap', rownames = F, options=list(buttons = c('csv','excel'), pageLength = 10, bPaginate = T, dom = 'Bfrtip') ) |> DT::formatStyle("gene_A", "prediction_percentile", color = "white", backgroundColor = DT::styleInterval( onc_enrich_report[['config']][['synleth']][['breaks']], onc_enrich_report[['config']][['synleth']][['colors']]) ) |> DT::formatStyle("gene_B", "prediction_percentile", color = "white", backgroundColor = DT::styleInterval( onc_enrich_report[['config']][['synleth']][['breaks']], onc_enrich_report[['config']][['synleth']][['colors']]) )
cat('\n <ul><li> <i> <span style="font-size: 105%; padding: 3px; background-color:#989898; color:white"> <b>NO</b> genes in the queryset are involved in synthetic lethality interactions for which <b>BOTH</b> member pairs are part of the queryset. </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
if(active_tab[['a_only']] == T){ cat("") cat("##### Single pair member in query set {.active}") cat("") }else{ cat("") cat("##### Single pair member in query set") cat("") }
sl_a <- crosstalk::SharedData$new(sl_interactions[['a_only']]) crosstalk::bscols( list( crosstalk::filter_select("gene_A", "Interactor A", sl_a, ~gene_A), crosstalk::filter_select("gene_B", "Interactor B", sl_a, ~gene_B), crosstalk::filter_slider("prediction_score", "Prediction score", sl_a, ~prediction_score, step = 0.025, min = 0.0, max = 0.45), crosstalk::filter_slider("prediction_percentile", "Prediction percentile", sl_a, ~prediction_percentile, min = 0.0, step = 2, max = 50) ), list( crosstalk::filter_slider("sequence_identity_pct", "Sequence identity (percent)", sl_a, ~sequence_identity_pct, min = 0, max = 100), crosstalk::filter_slider("family_size", "Gene family size", sl_a, ~family_size) ) ) htmltools::br() DT::datatable( sl_a, escape = F, extensions=c("Buttons","Responsive"), width = "100%", style = 'bootstrap', rownames = F, options=list(buttons = c('csv','excel'), pageLength = 10, bPaginate = T, dom = 'Bfrtip') ) |> DT::formatStyle("gene_A", "prediction_percentile", color = "white", backgroundColor = DT::styleInterval( onc_enrich_report[['config']][['synleth']][['breaks']], onc_enrich_report[['config']][['synleth']][['colors']]) )
cat('\n <ul><li> <i> <span style="font-size: 105%; padding: 3px; background-color:#989898; color:white"> <b>NO</b> genes in the queryset are involved in prediced synthetic lethal interactions for which <b>ONLY</b> a single member pair is part of the queryset. </span></i></li></ul>',sep='\n') cat('\n') cat('<br><br>')
Citation Note : If you use the output of the Synthetic lethality module of oncoEnrichR in your research, please cite the following resources and tools:
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