merged

.gitignore

@@ -3,4 +3,5 @@
 /.idea
 **/.pybiomart.sqlite
 **/__pycache__/
-/.DS_Store
+/.DS_Store
+**/.$*

README.md

@@ -28,7 +28,7 @@ for CellO:
 mkdir scratch/cello_resources
 curl https://deweylab.biostat.wisc.edu/cell_type_classification/resources_v2.0.0.tar.gz >scratch/cello_resources/resources_v2.0.0.tar.gz
 tar -C scratch/cello_resources -zxf scratch/cello_resources/resources_v2.0.0.tar.gz
-````
+```
 
 
 ```bash

cellenium_architecture.drawio

@@ -0,0 +1 @@
+<mxfile host="Electron" modified="2023-01-26T09:30:07.634Z" agent="5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) draw.io/20.7.4 Chrome/106.0.5249.199 Electron/21.3.3 Safari/537.36" version="20.7.4" etag="ZFWJRapDufXhwsbdNX54" type="device"><diagram id="5oOviqtw5uLLyDU2DDvS" name="Page-1">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</diagram></mxfile>

client/src/atoms.ts

@@ -5,6 +5,9 @@ import {
     AllGenesDocument,
     AllGenesQuery,
     AllGenesQueryVariables,
+    CellOAnnotationGroupIdDocument,
+    CellOAnnotationGroupIdQuery,
+    CellOAnnotationGroupIdQueryVariables,
     OmicsGeneFragment,
     StudyBasicsDocument,
     StudyBasicsFragment,
@@ -35,12 +38,12 @@ export const userGenesState = atom<Omics[]>({
     default: []
 })
 
-export const celltypeDiscoveryGenesState = atom<(Omics|null)[]>({
+export const celltypeDiscoveryGenesState = atom<(Omics | null)[]>({
     key: "celltypeDiscoveryGenesState",
     default: [null, null]
 })
 
-export const celltypeDiscoveryCoexpressionSamplesState = atom<(number[]|null)[]>({
+export const celltypeDiscoveryCoexpressionSamplesState = atom<(number[] | null)[]>({
     key: "celltypeDiscoveryCoexpressionSamplesState",
     default: [null]
 })
@@ -191,3 +194,17 @@ export const allGenesState = selector<Map<number, OmicsGeneFragment> | undefined
         }
     }
 });
+
+
+export const cellOAnnotationGroupIdState = selector<number | undefined>({
+    key: "cellOAnnotationGroupIdState",
+    get: async ({get}) => {
+        const annotationGroupIdData = await apolloClient.query<CellOAnnotationGroupIdQuery, CellOAnnotationGroupIdQueryVariables>({
+            query: CellOAnnotationGroupIdDocument,
+            fetchPolicy: 'no-cache'
+        });
+        if (annotationGroupIdData?.data) {
+            return annotationGroupIdData.data.annotationGroupsList[0].annotationGroupId;
+        }
+    }
+});

client/src/components/ExpressionDotPlot/ExpressionDotPlot.tsx

@@ -0,0 +1,68 @@
+import React, {useEffect, useMemo, useState} from 'react';
+import {VegaLite, View, VisualizationSpec} from "react-vega";
+import {DotPlotElementFragment} from "../../generated/types";
+import {ScenegraphEvent} from "vega";
+
+
+function createSpec(annotationTitle: string, xAxis: "studyName" | "displaySymbol") {
+    return {
+        "$schema": "https://vega.github.io/schema/vega-lite/v5.json",
+        "data": {"name": "table"},
+        "mark": {"type": "point", "filled": true},
+        "encoding": {
+            "y": {
+                "field": "annotationDisplayValue",
+                "type": "ordinal",
+                "title": annotationTitle
+            },
+            "x": xAxis === "studyName" ? {
+                "field": "studyName", "type": "nominal", "title": "Study",
+            } : {
+                "field": "displaySymbol", "type": "nominal", "title": "Gene",
+            },
+            "size": {
+                "field": "exprCellsFraction",
+                "type": "quantitative",
+                "title": "Expr. fraction"
+            },
+            "color": {
+                "field": "q3",
+                "type": "quantitative",
+                "scale": {"scheme": "viridis", reverse: true}
+            }
+
+        }
+    } as VisualizationSpec;
+}
+
+export function ExpressionDotPlot({
+                                      data,
+                                      annotationTitle,
+                                      xAxis,
+                                      onClick
+                                  }:
+                                      {
+                                          data: DotPlotElementFragment[],
+                                          annotationTitle: string,
+                                          xAxis: "studyName" | "displaySymbol",
+                                          onClick?: (dotPlotElement: DotPlotElementFragment, event: ScenegraphEvent) => void
+                                      }) {
+    const spec = useMemo(() => createSpec(annotationTitle, xAxis), [annotationTitle, xAxis]);
+
+    const setUpSelectionListener = (view: View) => {
+        view.addEventListener("click", (event, item) => {
+            if (item && onClick) {
+                const dotPlotElement = item.datum as DotPlotElementFragment;
+                onClick(dotPlotElement, event);
+            }
+        });
+    };
+
+    return <VegaLite
+        spec={spec}
+        onNewView={(view) => setUpSelectionListener(view)}
+        data={{
+            "table": data
+        }}/>
+}
+