Mouse Pansci

assets/json/mouse_pansci.json

@@ -0,0 +1,106 @@
+{
+    "version": "1.0.0",
+    "name": "Mouse Pansci",
+    "datasets": [
+        {
+            "uid": "mouse-pansci",
+            "name": "Mouse Pansci",
+            "files": [
+                {
+                    "type": "cells",
+                    "fileType": "anndata-cells.zarr",
+                    "url": "https://azimuth-vitessce.s3.us-west-2.amazonaws.com/mouse_pansci/vitessce_ref.zarr",
+                    "options": {
+                        "mappings": {
+                            "UMAP": {
+                                "key": "obsm/X_umap",
+                                "dims": [
+                                    0,
+                                    1
+                                ]
+                            }
+                        },
+                        "factors": [
+                            "obs/Main_cell_type",
+                            "obs/Sub_cell_type", 
+                            "obs/Sub_cell_type_organ"
+                        ]
+                    }
+                },
+                {
+                    "type": "cell-sets",
+                    "fileType": "anndata-cell-sets.zarr",
+                    "url": "https://azimuth-vitessce.s3.us-west-2.amazonaws.com/mouse_pansci/vitessce_ref.zarr",
+                    "options": [
+                        {
+                            "groupName": "Main_cell_type",
+                            "setName": "obs/Main_cell_type"
+                        },
+                        {
+                            "groupName": "Sub_cell_type",
+                            "setName": "obs/Sub_cell_type"
+                        },
+                        {
+                            "groupName": "Sub_cell_type_organ",
+                            "setName": "obs/Sub_cell_type_organ"
+                        }
+                    ]
+                },
+                {
+                    "type": "expression-matrix",
+                    "fileType": "anndata-expression-matrix.zarr",
+                    "url": "https://azimuth-vitessce.s3.us-west-2.amazonaws.com/mouse_pansci/vitessce_ref.zarr",
+                    "options": {
+                        "matrix": "X"
+                    }
+                }
+            ]
+        }
+    ],
+    "initStrategy": "auto",
+    "coordinationSpace": {
+        "embeddingType": {
+            "UMAP": "UMAP"
+        },
+        "embeddingCellRadius": {
+            "UMAP": 0.03
+        },
+        "embeddingCellSetLabelsVisible": {
+            "UMAP": true
+        },
+        "embeddingCellSetLabelSize": {
+            "UMAP": 10
+        }
+    },
+    "layout": [
+        {
+            "component": "cellSets",
+            "h": 3,
+            "w": 3,
+            "x": 9,
+            "y": 0,
+            "coordinationScopes": {}
+        },
+        {
+            "component": "genes",
+            "h": 3,
+            "w": 3,
+            "x": 9,
+            "y": 3,
+            "coordinationScopes": {}
+        },
+        {
+            "component": "scatterplot",
+            "h": 6,
+            "w": 9,
+            "x": 0,
+            "y": 0,
+            "coordinationScopes": {
+                "embeddingType": "UMAP",
+                "embeddingCellRadius": "UMAP",
+                "embeddingCellSetLabelsVisible": "UMAP",
+                "embeddingCellSetLabelSize": "UMAP"
+            }
+        }
+    ]
+}

assets/mouse_pansci.jsx

@@ -0,0 +1,22 @@
+const React = window.React;
+const ReactDOM = window.ReactDOM;
+const { Vitessce } = window.vitessce.index;
+import myViewConfig from 'json/mouse_pansci.json';
+
+function MyVitessce() {
+    return (
+        <div className="vitessce-app">
+            <Vitessce
+                config={myViewConfig}
+                height={800}
+                theme="dark"
+            />
+        </div>
+    );
+}
+
+function renderMyVitessce() {
+    ReactDOM.render(<MyVitessce />, document.getElementById("vitessce"));
+}
+
+renderMyVitessce();

content/_index.md

@@ -8,7 +8,7 @@ type: "static"
 Azimuth is a web application that uses an annotated reference dataset to <b>automate the processing, analysis, and interpretation of a new single-cell RNA-seq or ATAC-seq experiment</b>. Azimuth leverages a <b>'reference-based mapping'</b> pipeline that inputs a counts matrix and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery). All results can be explored within the app, and easily downloaded for additional downstream analysis.
 </p>
 
-The development of Azimuth is led by the New York Genome Center Mapping Component as part of the [NIH Human Biomolecular Atlas Project (HuBMAP)](https://commonfund.nih.gov/hubmap). Thirteen molecular reference maps are currently available, with more coming soon.
+The development of Azimuth is led by the New York Genome Center Mapping Component as part of the [NIH Human Biomolecular Atlas Project (HuBMAP)](https://commonfund.nih.gov/hubmap). Fourteen molecular reference maps are currently available, with more coming soon.
 
 {{< /section >}}
 

content/references/mouse_pansci/index.md

@@ -0,0 +1,11 @@
+---
+type: "static"
+----
+{{< section >}}
+
+# Mouse Pansci Reference Explorer
+
+{{< /section >}}
+
+{{< vitessce script="mouse_pansci.jsx" >}}
+{{< vitessce_marker_tables ref="Mouse - Pansci" >}}

data/azimuth_references.yaml

@@ -327,3 +327,22 @@
         file: tonsil_v2_l1.csv
       - name: celltype.l2
         file: tonsil_v2_l2.csv
+
+- title: Mouse - Pansci
+  applink: https://app.azimuth.hubmapconsortium.org/app/mouse_pansci
+  image: mousepansciumap.png
+  snakemake: https://github.com/satijalab/azimuth-references/tree/master/mouse_pansci
+  zenodo: TBD
+  vitessce: /references/mouse_pansci
+  modalities: RNA
+  unit: Cells
+  nunit: 488,526
+  species: Mouse
+  demodata: "[Emont et al., 2022.](https://www.nature.com/articles/s41586-022-04518-2)"
+  dataref: |
+      [Zhang et al., 2024](https://www.biorxiv.org/content/10.1101/2024.03.01.583001v1)
+  details: |
+          This reference consists of 488,526 cells, with a uniform subsample of 120 cells per subtype from the PanSci mouse organismal aging atlas. Cells were sourced from 14 mouse organs/tissue, including brain, lung, heart, liver, kidney, muscle, stomach, duodenum, jejunum, ileum, colon, brown adipose tissue, inguinal adipose tissue, gonadal adipose tissue, across three different genetic backgrounds: C57BL/6, B6.129S7-Rag1tm1Mom/J, and B6.Cg-Prkdcscid/SzJ. The library for each organ/tissue was constructed using a refined version of the EasySci protocol. Below, we include markers for only the "Main_cell_type" annotation level, which is the most general annotation level in the reference. There are also two more levels of annotation included in the azimuth app.
+  annotations:
+      - name: Main_cell_type
+        file: mouse_pansci_l1.csv