From 4e31d4ef794a0bf1abeec53cc1ab7aee819b7156 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Sun, 14 Aug 2022 18:04:40 +0200
Subject: [PATCH] Add rankings correlation plot

---
 R/server.R | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
 R/ui.R     | 54 +++++++++++++++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 101 insertions(+), 1 deletion(-)

diff --git a/R/server.R b/R/server.R
index c1ce3a9..33b17e1 100644
--- a/R/server.R
+++ b/R/server.R
@@ -116,6 +116,54 @@ server <- function(options) {
       geposan::plot_rankings(rankings, gene_sets)
     })
 
+    output$ranking_correlation_plot <- plotly::renderPlotly({
+      preset <- preset()
+      ranking <- ranking()
+
+      ranking_x <- if (input$ranking_x == "combined") {
+        ranking
+      } else {
+        weights <- list()
+        weights[[input$ranking_x]] <- 1.0
+        geposan::ranking(ranking, weights)
+      }
+
+      ranking_y <- if (input$ranking_y == "combined") {
+        ranking
+      } else {
+        weights <- list()
+        weights[[input$ranking_y]] <- 1.0
+        geposan::ranking(ranking, weights)
+      }
+
+      gene_sets <- list("Reference genes" = preset$reference_gene_ids)
+      comparison_gene_ids <- comparison_gene_ids()
+
+      if (length(comparison_gene_ids) >= 1) {
+        gene_sets <- c(
+          gene_sets,
+          list("Comparison genes" = comparison_gene_ids)
+        )
+      }
+
+      method_names <- geposan::all_methods() |> purrr::lmap(function(method) {
+        l <- list()
+        l[[method[[1]]$id]] <- method[[1]]$name
+        l
+      })
+
+      method_names[["combined"]] <- "Combined"
+
+      geposan::plot_rankings_correlation(
+        ranking_x,
+        ranking_y,
+        method_names[[input$ranking_x]],
+        method_names[[input$ranking_y]],
+        gene_sets = gene_sets,
+        use_ranks = input$use_ranks
+      )
+    })
+
     output$comparison_text <- renderUI({
       reference <- geposan::compare(
         ranking(),
diff --git a/R/ui.R b/R/ui.R
index e1179a1..a84d05b 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -4,6 +4,14 @@
 #'
 #' @noRd
 ui <- function(options) {
+  ranking_choices <- purrr::lmap(geposan::all_methods(), function(method) {
+    l <- list()
+    l[[method[[1]]$name]] <- method[[1]]$id
+    l
+  })
+
+  ranking_choices <- c(ranking_choices, "Combined" = "combined")
+
   div(
     custom_css(),
     shinyjs::useShinyjs(),
@@ -46,7 +54,7 @@ ui <- function(options) {
                 )
               ),
               tabPanel(
-                title = "Methods & Distribution",
+                title = "Method comparison",
                 div(
                   style = "margin-top: 16px",
                   plotly::plotlyOutput(
@@ -56,6 +64,50 @@ ui <- function(options) {
                   )
                 )
               ),
+              tabPanel(
+                title = "Method correlation",
+                div(
+                  style = "margin-top: 16px",
+                  div(
+                    class = "flow-layout",
+                    selectInput(
+                      "ranking_y",
+                      label = NULL,
+                      choices = ranking_choices
+                    ),
+                    span(
+                      style = paste0(
+                        "display: inline-block;",
+                        "margin-right: 12px;",
+                        "padding: 0.375rem 0.75rem;"
+                      ),
+                      "~"
+                    ),
+                    selectInput(
+                      "ranking_x",
+                      label = NULL,
+                      choices = ranking_choices,
+                      selected = "combined"
+                    ),
+                    div(
+                      style = paste0(
+                        "display: inline-block;",
+                        "padding: 0.375rem 0.75rem;"
+                      ),
+                      checkboxInput(
+                        "use_ranks",
+                        "Use ranks instead of scores",
+                        value = TRUE
+                      )
+                    )
+                  ),
+                  plotly::plotlyOutput(
+                    "ranking_correlation_plot",
+                    width = "100%",
+                    height = "600px"
+                  )
+                )
+              ),
               tabPanel(
                 title = "Comparison",
                 div(