diff --git a/R/server.R b/R/server.R index a7488cc..e5e21b1 100644 --- a/R/server.R +++ b/R/server.R @@ -107,44 +107,6 @@ server <- function(input, output, session) { geposan::plot_positions(preset$species_ids, gene_sets) }) - output$assessment_synopsis <- renderText({ - reference_gene_ids <- preset()$reference_gene_ids - - included_reference_count <- results_filtered()[ - gene %chin% reference_gene_ids, - .N - ] - - reference_results <- results()[gene %chin% reference_gene_ids] - total_reference_count <- nrow(reference_results) - - if (total_reference_count > 0) { - mean_rank <- as.character(round( - reference_results[, mean(rank)], - digits = 1 - )) - - min_rank <- as.character(reference_results[, min(rank)]) - max_rank <- as.character(reference_results[, max(rank)]) - } else { - mean_rank <- "Unknown" - min_rank <- "Unknown" - max_rank <- "Unknown" - } - - sprintf( - "Included reference genes: %i/%i
\ - Mean rank of reference genes: %s
\ - First rank of reference genes: %s
\ - Last rank of reference genes: %s", - included_reference_count, - total_reference_count, - mean_rank, - min_rank, - max_rank - ) - }) - output$rank_plot <- plotly::renderPlotly({ preset <- preset() gene_sets <- list("Reference genes" = preset$reference_gene_ids) @@ -210,10 +172,6 @@ server <- function(input, output, session) { geposan::plot_boxplot(ranking(), gene_sets) }) - output$chromosome_plot <- plotly::renderPlotly({ - geposan::plot_chromosomes(ranking()) - }) - output$gost <- plotly::renderPlotly({ if (input$enable_gost) { result <- gprofiler2::gost( diff --git a/R/ui.R b/R/ui.R index a5c5b5c..12ef353 100644 --- a/R/ui.R +++ b/R/ui.R @@ -8,7 +8,7 @@ ui <- div( primary = "#1c71d8" ), title = "TPE-OLD candidates", - selected = "Ranking", + selected = "Results", tabPanel( "Input data", sidebarLayout( @@ -28,7 +28,7 @@ ui <- div( ), ), tabPanel( - "Ranking", + "Results", sidebarLayout( sidebarPanel( width = 3, @@ -37,68 +37,74 @@ ui <- div( ), mainPanel( width = 9, - div( - style = "margin-top: 16px", - plotly::plotlyOutput( - "rank_plot", - width = "100%", - height = "600px" + tabsetPanel( + type = "pills", + tabPanel( + title = "Overview", + div( + style = "margin-top: 16px", + plotly::plotlyOutput( + "rank_plot", + width = "100%", + height = "600px" + ) + ) + ), + tabPanel( + title = "Methods & Distribution", + div( + style = "margin-top: 16px", + plotly::plotlyOutput( + "rankings_plot", + width = "100%", + height = "600px" + ) + ) + ), + tabPanel( + title = "Comparison", + div( + style = "margin-top: 16px", + plotly::plotlyOutput( + "boxplot", + width = "100%", + height = "600px" + ) + ) + ), + tabPanel( + title = "Detailed results", + div( + style = "margin-top: 16px", + uiOutput("copy"), + ), + div( + style = "margin-top: 16px", + DT::DTOutput("genes") + ) + ), + tabPanel( + title = "g:Profiler", + checkboxInput( + "enable_gost", + "Perform a gene set enrichment analysis on the \ + filtered result genes." + ), + conditionalPanel( + "input.enable_gost == true", + plotly::plotlyOutput( + "gost", + width = "100%", + height = "600px" + ) + ) ) - ), - div( - style = "margin-top: 16px", - plotly::plotlyOutput( - "rankings_plot", - width = "100%", - height = "600px" - ) - ), + ) ) - ), - ), - tabPanel( - "Detailed results", - uiOutput("copy"), - div( - style = "margin-top: 16px", - DT::DTOutput("genes") ) ), tabPanel( - "Assessment", - htmlOutput("assessment_synopsis"), - div( - style = "margin-top: 16px", - plotly::plotlyOutput( - "boxplot", - width = "100%", - height = "600px" - ) - ), - div( - style = "margin-top: 16px", - plotly::plotlyOutput( - "chromosome_plot", - width = "100%", - height = "600px" - ) - ), - ), - tabPanel( - "Analysis", - checkboxInput( - "enable_gost", - "Perform a gene set enrichment analysis on the \ - filtered result genes." - ), - conditionalPanel( - "input.enable_gost == true", - plotly::plotlyOutput( - "gost", - width = "100%", - height = "600px" - ) - ) + title = "Publication" ) ) )