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HautaniemiLab · Jan 23, 2025 · 113f693 · 113f693
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Showing 20 changed files with 89 additions and 25 deletions.
diff --git a/404.html b/404.html
diff --git a/LICENSE-text.html b/LICENSE-text.html
diff --git a/LICENSE.html b/LICENSE.html
diff --git a/articles/index.html b/articles/index.html
diff --git a/articles/introduction.html b/articles/introduction.html
diff --git a/articles/introduction_files/jellyfisher-binding-1.0.0/jellyfisher.js b/articles/introduction_files/jellyfisher-binding-1.0.0/jellyfisher.js
@@ -0,0 +1,32 @@
+HTMLWidgets.widget({
+  name: "jellyfisher",
+
+  type: "output",
+
+  factory: function (el, width, height) {
+    return {
+      renderValue: function (x) {
+        // Ensure that absolute positioning works in R markdown
+        el.style.position = "relative";
+
+        jellyfish.setupGui(
+          el,
+          {
+            samples: HTMLWidgets.dataframeToD3(x.tables.samples),
+            phylogeny: HTMLWidgets.dataframeToD3(x.tables.phylogeny),
+            compositions: HTMLWidgets.dataframeToD3(x.tables.compositions),
+            ranks: x.tables.ranks
+              ? HTMLWidgets.dataframeToD3(x.tables.ranks)
+              : null,
+          },
+          x.options,
+          x.controls
+        );
+      },
+
+      resize: function (width, height) {
+        // TODO: code to re-render the widget with a new size
+      },
+    };
+  },
+});
diff --git a/authors.html b/authors.html
diff --git a/index.html b/index.html
diff --git a/pkgdown.yml b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   introduction: introduction.html
-last_built: 2025-01-23T12:30Z
+last_built: 2025-01-23T12:43Z
 urls:
   reference: https://hautaniemilab.github.io/jellyfisher/reference
   article: https://hautaniemilab.github.io/jellyfisher/articles
diff --git a/reference/extract_tables_from_clonevol.html b/reference/extract_tables_from_clonevol.html
diff --git a/reference/index.html b/reference/index.html
diff --git a/reference/jellyfisher-shiny.html b/reference/jellyfisher-shiny.html
diff --git a/reference/jellyfisher.html b/reference/jellyfisher.html
diff --git a/reference/jellyfisher_example_tables.html b/reference/jellyfisher_example_tables.html
diff --git a/reference/libs/jellyfisher-binding-1.0.0/jellyfisher.js b/reference/libs/jellyfisher-binding-1.0.0/jellyfisher.js
@@ -0,0 +1,32 @@
+HTMLWidgets.widget({
+  name: "jellyfisher",
+
+  type: "output",
+
+  factory: function (el, width, height) {
+    return {
+      renderValue: function (x) {
+        // Ensure that absolute positioning works in R markdown
+        el.style.position = "relative";
+
+        jellyfish.setupGui(
+          el,
+          {
+            samples: HTMLWidgets.dataframeToD3(x.tables.samples),
+            phylogeny: HTMLWidgets.dataframeToD3(x.tables.phylogeny),
+            compositions: HTMLWidgets.dataframeToD3(x.tables.compositions),
+            ranks: x.tables.ranks
+              ? HTMLWidgets.dataframeToD3(x.tables.ranks)
+              : null,
+          },
+          x.options,
+          x.controls
+        );
+      },
+
+      resize: function (width, height) {
+        // TODO: code to re-render the widget with a new size
+      },
+    };
+  },
+});
diff --git a/reference/select_patients.html b/reference/select_patients.html