Merge pull request #193 from higlass/kerpedji/sequence-logo-and-multivec-docs

fix,docs: Updated docs for multivec tracks and added a literal for sequence-log…

Author: pkerpedjiev

deno.json

@@ -1,5 +1,9 @@
 {
   "lock": false,
+  "imports": {
+    "higlass": "https://esm.sh/[email protected]?deps=react@17,react-dom@17,pixi.js@6",
+    "@lukeed/uuid": "https://esm.sh/@lukeed/[email protected]"
+  },
   "compilerOptions": {
     "checkJs": true,
     "lib": ["dom", "dom.iterable", "esnext"]

docs/examples.rst

@@ -54,18 +54,7 @@ visualization with ``hg.Viewconf.locks()``.
 Multivec Files
 ---------------
 
-To view multivec files, we have to load the higlass plugin track. Execute the following code in a cell in the Jupyter notebook you're using.
-
-.. code-block:: javascript
-
-    %%javascript
-
-    require(["https://unpkg.com/higlass-multivec/dist/higlass-multivec"],
-        function(hglib) {
-
-    });
-
-Create the multivec and output file:
+To view multivec files, create the multivec and output file:
 
 .. code-block:: python
 
@@ -84,7 +73,8 @@ Create the multivec and output file:
     )
 
 
-Create the viewer:
+Create the viewer. The `horizontal-stacked-bar` track is a plugin track so we
+have to pass in its url so higlass knows where to load it.
 
 .. code-block:: python
 
@@ -93,7 +83,9 @@ Create the viewer:
     ts = multivec(output_file)
     view = hg.view(
         hg.track("top-axis", height=20),
-        ts.track("horizontal-stacked-bar", height=50),
+        ts.track("horizontal-stacked-bar", height=50,
+            plugin_url="https://unpkg.com/higlass-multivec/dist/higlass-multivec"
+        ),
     )
     view.domain(x=[0, 1000000])
 

src/higlass/_utils.py

@@ -32,6 +32,7 @@
     "viewport-projection-horizontal": "top",
     "vertical-chromosome-labels": "left",
     "vertical-gene-annotations": "left",
+    "sequence-logo": "top",
 }
 
 datatype_default_track = {

src/higlass/api.py

@@ -730,7 +730,7 @@ def view(
             else:
                 position = utils.track_default_position.get(track.type)
                 if position is None:
-                    raise ValueError("No default track type")
+                    raise ValueError(f"No position for track type: {track.type}")
 
             data[position].append(track)
 

src/higlass/widget.js

@@ -1,5 +1,5 @@
-import * as hglib from "https://esm.sh/higlass@1.13?deps=react@17,react-dom@17,pixi.js@6";
-import { v4 } from "https://esm.sh/@lukeed/uuid@2.0.1";
+import * as hglib from "higlass";
+import { v4 } from "@lukeed/uuid";
 
 /** @import { HGC, PluginDataFetcherConstructor, GenomicLocation, Viewconf, DataFetcher} from "./types.ts" */