From 9ad5fde62f59be87b777f75663f0c4ba103afde8 Mon Sep 17 00:00:00 2001
From: ArtPoon <artpoon@gmail.com>
Date: Tue, 7 May 2024 13:25:59 -0400
Subject: [PATCH] fixes #497 and #524

---
 index-es.html  |  2 +-
 index-fr.html  |  2 +-
 index-zh.html  |  4 ++--
 index.html     |  2 +-
 js/covizu.js   | 15 +++++++++++++--
 js/drawtree.js |  4 ++--
 6 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/index-es.html b/index-es.html
index fcb8b1b..b7d7a64 100644
--- a/index-es.html
+++ b/index-es.html
@@ -39,7 +39,7 @@
       sample_legend: "Tamaño de la muestra (log10)",
       coldate_legend: "Colección mas reciente",
       diverge_legend: "Divergencia (reloj molecular estricto)",
-      infections_legend: "Infecciones previstas (en aumento)",
+      infections_legend: "Infecciones previstas (log10, en aumento)",
       infections_tooltip: "Infecciones previstas",
       total: "Total",
       sampled: "Muestreadas",
diff --git a/index-fr.html b/index-fr.html
index 6e52651..71f8e2f 100644
--- a/index-fr.html
+++ b/index-fr.html
@@ -39,7 +39,7 @@
       sample_legend: "Taille de l'échantillon (log10)",
       coldate_legend: "Date des échantillons les plus récents",
       diverge_legend: "Divergence (prédiction par horloge moléculaire stricte)",
-      infections_legend: "Infections prévues (en augmentation)",
+      infections_legend: "Infections prévues (log10, en augmentation)",
       infections_tooltip: "Infections prévues",
       total: "Total",
       sampled: "Échantillonné",
diff --git a/index-zh.html b/index-zh.html
index 1d03d37..986fbe8 100644
--- a/index-zh.html
+++ b/index-zh.html
@@ -37,10 +37,10 @@
         "Oceania": "大洋洲",
         "South America": "南美"
       },
-      sample_legend: "样本大小 (log10)",
+      sample_legend: "样本大小 (常用对数)",
       coldate_legend: "最后收集日期",
       diverge_legend: "趋异 (严格分子钟)",
-      infections_legend: "预测感染病例（增加中)",
+      infections_legend: "预测感染病例（常用对数, 增加中)",
       infections_tooltip: "预测感染病例",
       total: "总计",
       sampled: "采样",
diff --git a/index.html b/index.html
index 141594a..8f4b539 100644
--- a/index.html
+++ b/index.html
@@ -39,7 +39,7 @@
       sample_legend: "Sample size (log10)",
       coldate_legend: "Last collection date",
       diverge_legend: "Divergence (strict molecular clock)",
-      infections_legend: "Predicted infections (increasing)",
+      infections_legend: "Predicted infections (log10, increasing)",
       infections_tooltip: "Predicted infections",
       total: "Total",
       sampled: "Sampled",
diff --git a/js/covizu.js b/js/covizu.js
index 6a9f3c0..9817013 100644
--- a/js/covizu.js
+++ b/js/covizu.js
@@ -1018,11 +1018,22 @@ function export_csv() {
   var all_tips = [...tips, ...recombinant_tips, ...df_xbb];
 
   // write lineage-level information to CSV file for download
-  var csvFile = 'lineage,mean.diffs,clock.residual,num.cases,num.variants,min.coldate,max.coldate,mean.coldate';
+  var csvFile = 'lineage,mean.diffs,clock.residual,num.cases,num.variants,min.coldate,max.coldate,' +
+      'mean.coldate,pred.cases';
   var lineage_info = []
   for (tip of all_tips) {
     if (tip.isTip === undefined || tip.isTip)
-      lineage_info.push([`${tip.thisLabel === undefined ? tip.label1 : tip.thisLabel},${Math.round(100*tip.mean_ndiffs)/100.},${Math.round(100*tip.residual)/100.},${tip.nsamples},${tip.varcount},${formatDate(tip.first_date)},${formatDate(tip.last_date)},${formatDate(tip.mcoldate)}`]);
+      lineage_info.push([
+        tip.thisLabel === undefined ? tip.label1 : tip.thisLabel,
+        Math.round(100*tip.mean_ndiffs)/100.,
+        Math.round(100*tip.residual)/100.,
+        tip.nsamples,
+        tip.varcount,
+        formatDate(tip.first_date),
+        formatDate(tip.last_date),
+        formatDate(tip.mcoldate),
+        Math.round(tip.infections)
+       ]);
   }
   csvFile = csvFile + "\n" + lineage_info.join("\n");
   blob = new Blob([csvFile], {type: "text/csv"});
diff --git a/js/drawtree.js b/js/drawtree.js
index 03a4aa3..52fa274 100644
--- a/js/drawtree.js
+++ b/js/drawtree.js
@@ -418,7 +418,7 @@ function draw_clusters(tips, filtered_recombinant_tips, redraw=false) {
   diverge_pal = d3.scaleSequential(d3.interpolatePlasma)
       .domain(d3.extent(tip_obj, function(d) { return d.residual; }));
   infections_pal = d3.scaleSequential(d3.interpolateViridis)
-      .domain([0, d3.max(tip_obj, function(d) { return d.infections; })]);
+      .domain([0, d3.max(tip_obj, function(d) { return Math.log10(d.infections); })]);
 
   generate_legends();
   changeTreeColour();
@@ -521,7 +521,7 @@ function changeTreeColour() {
           }
           else if (opt === "Infections") {
             $("div#svg-infections-legend").show();
-            if (d.infections > 0) return infections_pal(d.infections);
+            if (d.infections > 0) return infections_pal(Math.log10(d.infections));
             else if (d.infections == 0) return null_infections_colour;
             else return dsc_infections_colour;
           }