From fffc0aedf8ecbadcf1d7b13af0ab88fb0ed9bee1 Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Fri, 13 Sep 2024 09:24:28 -0500
Subject: [PATCH] Show all candidates from peptide table in the anchor heatmap
 plot

---
 pvactools/tools/pvacview/server.R | 17 ++++++++++++++---
 pvactools/tools/pvacview/ui.R     |  6 +++---
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/pvactools/tools/pvacview/server.R b/pvactools/tools/pvacview/server.R
index 79ee9332..d224e164 100644
--- a/pvactools/tools/pvacview/server.R
+++ b/pvactools/tools/pvacview/server.R
@@ -930,6 +930,9 @@ server <- shinyServer(function(input, output, session) {
   })
   ##Add legend for anchor heatmap
   output$peptideFigureLegend <- renderPlot({
+    if (is.null(df$metricsData)) {
+      return()
+    }
     colors <- colorRampPalette(c("lightblue", "blue"))(99)[seq(1, 99, 7)]
     color_pos <- data.frame(d = as.character(seq(1, 99, 7)), x1 = seq(0.1, 1.5, 0.1), x2 = seq(0.2, 1.6, 0.1), y1 = rep(1, 15), y2 = rep(1.1, 15), colors = colors)
     color_label <- data.frame(x = c(0.1, 0.8, 1.6), y = rep(0.95, 3), score = c(0, 0.5, 1))
@@ -944,7 +947,15 @@ server <- shinyServer(function(input, output, session) {
     print(p1)
   })
   ##Anchor Heatmap overlayed on selected peptide sequences
-  output$anchorPlot <- renderPlot({
+  anchorPlotHeight <- reactive({
+    if (is.null(df$metricsData)) {
+      return(0)
+    }
+    peptide_data <- df$metricsData[[selectedID()]]$good_binders[[selectedTranscriptSet()]]$`peptides`
+    peptide_names <- names(peptide_data)
+    (length(peptide_names)) * 2 * 15
+  })
+  observe({output$anchorPlot <- renderPlot({
     if (is.null(df$metricsData)) {
       return()
     }
@@ -964,7 +975,7 @@ server <- shinyServer(function(input, output, session) {
           peptide_data[[peptide_names[[i]]]]$individual_el_percentile_calls <- NULL
         }
         peptide_data <- as.data.frame(peptide_data)
-        p1 <- ggplot() + scale_x_continuous(limits = c(0, 80)) + scale_y_continuous(limits = c(-31, 1))
+        p1 <- ggplot() + scale_x_continuous(limits = c(0, 80)) + scale_y_continuous(limits = c((length(peptide_names) * 2 + 1) * -1, 1))
         all_peptides <- list()
         incProgress(0.1)
         for (i in 1:length(peptide_names)) {
@@ -1028,7 +1039,7 @@ server <- shinyServer(function(input, output, session) {
         print(p1)
       }
     })
-  }, height = 400, width = 800)
+  }, height = anchorPlotHeight(), width = 800)})
   #anchor score tables for each HLA allele
   output$anchorWeights<- renderDT({
     withProgress(message = "Loading Anchor Weights Table", value = 0, {
diff --git a/pvactools/tools/pvacview/ui.R b/pvactools/tools/pvacview/ui.R
index 59ff09d9..7f71e7c0 100644
--- a/pvactools/tools/pvacview/ui.R
+++ b/pvactools/tools/pvacview/ui.R
@@ -224,9 +224,9 @@ explore_tab <- tabItem(
                         fluidRow(
                             column(width = 6,
                                    div(style = 'overflow-y:scroll;height: 500px;',
-                                       h4("Allele specific anchor prediction heatmap for top 15 candidates in peptide table."),
-                                       h5("HLA allele specific anchor predictions overlaying good-binding peptide sequences generated from each specific transcript.", br(),
-                                          " Current version supports the first 15 MT/WT peptide sequence pairs (first 30 rows of the peptide table)."), br(),
+                                       h4("Allele specific anchor prediction heatmap for the candidates in peptide table."),
+                                       h5("HLA allele specific anchor predictions overlaying candidate peptide sequences for selected transcript set."),
+                                       br(),
                                        plotOutput(outputId = "peptideFigureLegend", height = "50px"),
                                        plotOutput(outputId = "anchorPlot")
                                    )