Add doc for chromsizes grid overlay (#187)

Author: pkerpedjiev

README.md

@@ -86,6 +86,7 @@ All commands are run from the root of the project, from a terminal:
 
 | Command                                         | Action                                        |
 | ----------------------------------------------- | --------------------------------------------- |
+| `uv run jupyter lab`                            | Run Jupyter lab with current package state    |
 | `uv run ruff check --fix && uv run ruff format` | Lint and apply formatting                     |
 | `uv run check`                                  | Check linting rules                           |
 | `uv run ruff format --check`                    | Check formatting                              |
@@ -112,13 +113,15 @@ Releases are managed via the GitHub UI.
 [Draft a new release](https://github.com/higlass/higlass-python/releases/new):
 
 1. **Create a tag**
+
    - Click _"Choose a tag"_, then **type a new tag** in the format
      `v[major].[minor].[patch]` to create it.
    - _Note_: The UI is not obvious about this. You can create a tag here, not
      just select one. Tag creation triggers a
      [workflow](.github/workflows/ci.yml) to publish to PyPI.
 
 2. **Generate release notes**
+
    - Click _"Generate Release Notes"_ to auto-summarize changes from merged PRs.
    - Edit to exclude irrelevant changes for end users (e.g., docs or CI).
 

docs/getting_started.rst

@@ -285,6 +285,28 @@ Tracks may be combined with the ``hg.combine()`` utility:
 
    hg.view((combined_track, "top")).domain(x=[0, 1e9])
 
+Chromosome grid on a heatmap
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: python
+
+    import higlass as hg
+
+    cs_ts = hg.chromsizes('chromSizes_hg19_reordered.tsv')
+    cool_ts = hg.cooler("Dixon2012-J1-NcoI-R1-filtered.100kb.multires.cool")
+
+    hg.view(
+        (hg.combine(
+            cool_ts.track(options={"name": "blah"}),
+            cs_ts.track('2d-chromosome-grid'),
+        position='center'), 'center'),
+        (cs_ts.track('horizontal-chromosome-labels'), 'top'),
+        (cs_ts.track('horizontal-chromosome-labels'), 'left'),
+        width=6)
+
+.. image:: img/chromsizes-overlay.png
+    :align: center
+    :width: 250
 
 Multiple Views
 --------------

docs/higlass_theme/static/higlass.css

@@ -800,3 +800,9 @@ div.document {
     position: static;
   }
 }
+
+img.align-center {
+  margin-left: auto;
+  margin-right: auto;
+  display: block;
+}

docs/img/chromsizes-overlay.png

@@ -35,6 +35,7 @@
     bed2ddb,
     beddb,
     bigwig,
+    chromsizes,
     cooler,
     hitile,
     multivec,

src/higlass/__init__.py

@@ -191,6 +191,14 @@ def load(filepath: str | pathlib.Path) -> ClodiusTileset:
     return load
 
 
+def chromsizes(filepath: str) -> ClodiusTileset:
+    from clodius.tiles.chromsizes import tileset_info
+
+    return ClodiusTileset(
+        datatype="chromsizes", tiles_impl=None, info_impl=lambda: tileset_info(filepath)
+    )
+
+
 bed2ddb = create_lazy_clodius_loader("bed2ddb", datatype="2d-rectangle-domains")
 beddb = create_lazy_clodius_loader("beddb", datatype="vector")
 bigwig = create_lazy_clodius_loader("bigwig", datatype="vector")