DEGA-297-update-docs (#211)

* update widget.js docs asset

* working on gallery

* working on gallery

* adding Pancreas gallery example

* updating gallery

* adding tutorial notebooks

* added chrmoium tutorial notebook

* adding tutorial notebooks

* added notebooks

* removed print statement

* Update docs/assets/js/gallery_visium_hd_pancreas.js

Co-authored-by: Copilot <[email protected]>

* Update docs/assets/js/gallery_visium_hd_human_kidney.js

Co-authored-by: Copilot <[email protected]>

---------

Co-authored-by: Copilot <[email protected]>

Author: cornhundred

docs/assets/img/visium_hd_human_kidney.png

@@ -0,0 +1,45 @@
+import celldega from './widget.js';
+document.addEventListener("DOMContentLoaded", async () => {
+
+    const landscape_el = document.getElementById('landscape-visium-hd-human-kidney');
+
+    if (window.location.pathname.endsWith('gallery_visium_hd_human_kidney/')){
+
+        console.log('hi!')
+        // Use the imported functions
+        const token = '';
+        const ini_zoom = -3.5;
+        const ini_x = 3000;
+        const ini_y = 3000;
+        const ini_z = 0;
+        const base_url = 'https://raw.githubusercontent.com/broadinstitute/Celldega_Visium_HD_Human_Kidney_FFPE/main/Visium_HD_Human_Kidney_FFPE';
+
+        const landscape = await celldega.landscape_sst(
+            // ini_model
+            {},
+            // element
+            landscape_el,
+            // base_url
+            base_url,
+            // token
+            token,
+            // initial coordinates
+            ini_x,
+            ini_y,
+            ini_z,
+            ini_zoom,
+            // square_tile_size (hardwired to 1.4 for this dataset)
+            1.4,
+            // dataset_name
+            '',
+            // width
+            '100%',
+            // height
+            '100%',
+            // creds
+            {},
+        );
+
+    }
+
+});

docs/assets/img/visium_hd_pancreas.png

@@ -0,0 +1,45 @@
+import celldega from './widget.js';
+document.addEventListener("DOMContentLoaded", async () => {
+
+    const landscape_el = document.getElementById('landscape-visium-hd-pancreas');
+
+    if (window.location.pathname.endsWith('gallery_visium_hd_pancreas/')){
+
+        console.log('hi!')
+        // Use the imported functions
+        const token = '';
+        const ini_zoom = -3.5;
+        const ini_x = 3000;
+        const ini_y = 3000;
+        const ini_z = 0;
+        const base_url = 'https://raw.githubusercontent.com/broadinstitute/celldega_Visium_HD_Human_Pancreas_binned_outputs/main/Visium_HD_Human_Pancreas_binned_outputs';
+
+        const landscape = await celldega.landscape_sst(
+            // ini_model
+            {},
+            // element
+            landscape_el,
+            // base_url
+            base_url,
+            // token
+            token,
+            // initial coordinates
+            ini_x,
+            ini_y,
+            ini_z,
+            ini_zoom,
+            // square_tile_size (hardwired to 1.4 for this dataset)
+            1.4,
+            // dataset_name
+            '',
+            // width
+            '100%',
+            // height
+            '100%',
+            // creds
+            {},
+        );
+
+    }
+
+});

docs/assets/js/gallery_visium_hd_human_kidney.js

@@ -1,8 +1,17 @@
 # Jupyter Notebook Examples
 
+## Tutorials
+[Scanpy-Squidpy_Xenium_Pancreas](tutorial_notebooks/Scanpy-Squidpy_Xenium_Pancreas.ipynb)
+
+[Scanpy_Chromium](tutorial_notebooks/Scanpy_Chromium.ipynb)
+
+[Single-Cell Clustergram Chromium](tutorial_notebooks/Single-Cell_Clustergram_Chromium.ipynb)
+
 ## Brief Notebooks
 [Landscape View Xenium](brief_notebooks/Landscape_View_Xenium.ipynb)
 
 [Mouse-Brain_Alpha-Shape-Neighborhood](brief_notebooks/Mouse-Brain_Alpha-Shape-Neighborhood.ipynb)
 
-[Custom Segmentation Visualization in Celldega](brief_notebooks/Custom_Segmentation.ipynb)
+[Custom Segmentation Visualization in Celldega](brief_notebooks/Custom_Segmentation.ipynb)
+
+[Landscape-Clustergram_Visium-HD_Human_Lung_Cancer](brief_notebooks/Landscape-Clustergram_Visium-HD_Human_Lung_Cancer.ipynb)