Merge pull request #53 from broadinstitute/DEGA-138-Clustergrammer-PY

bringing in Clustergrammer-PY back-end

Author: cornhundred

docs/python/clust/api.md

@@ -0,0 +1,3 @@
+# Clust Module API Reference
+
+::: celldega.clust

docs/python/index.md

@@ -1,13 +1,13 @@
 # Python API Overview
 
-## [Neighborhood Overview](nbhd/api)
-The `nbhd` module contains methods for calculating tissue neighborhoods.
-
 ## [Pre Module Overview](pre/api)
-
 The `pre` module contains methods for pre-processing LandscapeFiles.
 
+## [Clust Module Overview](clust/api)
+The `clust` module contains methods for clustering high-dimensional data.
 
-## [Viz Module Overview](viz/api)
+## [Neighborhood Overview](nbhd/api)
+The `nbhd` module contains methods for calculating tissue neighborhoods.
 
+## [Viz Module Overview](viz/api)
 The `viz` module contains functions and classes for data visualization.

docs/python/nbhd/api.md

@@ -1,5 +1,3 @@
 # Neighborhood Module API Reference
 
-<!-- ::: celldega.pre.landscape -->
-<!-- ::: celldega.pre -->
 ::: celldega.nbhd

docs/python/viz/api.md

@@ -2,5 +2,5 @@
 
 ## Widget Classes
 
-::: celldega.viz.widget
+::: celldega.viz
 

js/deck-gl/make_tooltip.js

@@ -8,8 +8,6 @@ export const make_tooltip = (viz_state, info) => {
     let inst_name = ''
     let inst_cat = ''
 
-    console.log(info.layer.id)
-
     if (info.layer.id.startsWith('cell-layer') || info.layer.id.startsWith('path-layer')) {
         inst_name = info.layer.id.startsWith('cell-layer') ? viz_state.cats.cell_names_array[info.index] : viz_state.cats.polygon_cell_names[info.index]
         inst_cat = viz_state.cats.dict_cell_cats[inst_name]
@@ -26,8 +24,16 @@ export const make_tooltip = (viz_state, info) => {
         inst_html = `<div>neighborhood: ${inst_name}</div><div>cluster: ${inst_cat}</div>`
     }
 
-    d3.selectAll('.deck-tooltip')
-      .style('margin-top', '75px')
+    // d3.selectAll('.deck-tooltip')
+    //   .style('margin-top', '75px')
+
+    // console.log(viz_state.root)
+
+    // select the parent element of .deck-tooltip within viz_state.root
+    const tooltipContainer = viz_state.root.querySelector('.deck-tooltip');
+    tooltipContainer.style.marginTop = '50px'
+    const tooltipParent = tooltipContainer.parentElement.parentElement;
+    tooltipParent.style.position = 'unset'
 
     return {
         html: inst_html,

js/deck-gl/matrix/matrix_tooltip.js

@@ -4,8 +4,11 @@ export const get_tooltip = (viz_state, params) => {
 
     const {object, layer} = params;
 
-    d3.selectAll('.deck-tooltip')
-      .style('margin-top', '50px')
+    // select the parent element of .deck-tooltip within viz_state.root
+    const tooltipContainer = viz_state.root.querySelector('.deck-tooltip');
+    tooltipContainer.style.marginTop = '50px'
+    const tooltipParent = tooltipContainer.parentElement.parentElement;
+    tooltipParent.style.position = 'unset'
 
     if (object) {
       // Check which layer the tooltip is currently over

js/viz/landscape_ist.js

@@ -51,6 +51,8 @@ export const landscape_ist = async (
 
     let viz_state = {}
 
+    viz_state.root = el
+
     viz_state.buttons = {}
     viz_state.buttons.blue = '#8797ff'
     viz_state.buttons.gray = 'gray'

mkdocs.yaml

@@ -22,6 +22,8 @@ nav:
   - Python API:
       - python/index.md
       - pre: python/pre/api.md
+      - clust: python/clust/api.md
+      - nbhd: python/nbhd/api.md
       - viz: python/viz/api.md
 
   - JavaScript API:
@@ -39,6 +41,7 @@ nav:
     - examples/index.md
     - Brief Notebooks:
       - Landscape View Xenium: examples/brief_notebooks/Landscape_View_Xenium.ipynb
+      - Landscape-Matrix View Xenium: examples/brief_notebooks/Landscape-Matrix_Xenium.ipynb
       - Pre-Process LandscapeFiles: examples/brief_notebooks/Pre-process_Xenium_V1_human_Pancreas_FFPE_outs.ipynb
     # - Tutorials:
     #     - examples/Landscape_View_Xenium.ipynb

pyproject.toml

@@ -17,7 +17,6 @@ dependencies = [
     "imagecodecs~=2024.1.1",
     "scanpy~=1.10.2",
     "squidpy~=1.5.0",
-    "clustergrammer2==0.18.0",
     "shapely~=2.0.5",
     "polars~=1.10.0",
     "libpysal~=4.8.1"

src/celldega/__init__.py

@@ -4,6 +4,8 @@
 from celldega.pre import landscape
 from celldega.nbhd import alpha_shape
 
+from celldega.clust import Network
+
 # temporary fix for libpysal warning
 import warnings
 warnings.filterwarnings("ignore", category=FutureWarning)