Fix tracks

weng-lab · Apr 26, 2024 · 1d8f847 · 1d8f847
1 parent 599f6ec
commit 1d8f847
Show file tree

Hide file tree

Showing 8 changed files with 233 additions and 185 deletions.
diff --git a/immuscreen/package.json b/immuscreen/package.json
@@ -1,5 +1,5 @@
 {
-  "name": "screen2.0",
+  "name": "igscreen",
   "version": "0.1.0",
   "private": true,
   "scripts": {
@@ -68,7 +68,7 @@
     "eslint": "8.47.0",
     "eslint-config-next": "13.4.19",
     "graphql": "^16.7.1",
-    "jubilant-carnival": "^0.2.8",
+    "jubilant-carnival": "^0.6.0",
     "logojs-react": "^2.1.1",
     "next": "14.1.0",
     "normalize.css": "^8.0.1",
@@ -84,7 +84,7 @@
     "tailwindcss": "3.3.3",
     "typescript": "5.1.6",
     "umap-js": "^1.3.3",
-    "umms-gb": "^3.9.13",
+    "umms-gb": "^3.10.0",
     "uuid": "^9.0.1"
   },
   "devDependencies": {

diff --git a/immuscreen/src/app/celllineage/utils.ts b/immuscreen/src/app/celllineage/utils.ts
@@ -1,6 +1,11 @@
 import { cellTypeStaticInfo } from "../../common/consts";
 import { CellDisplayName, CellLineageTreeState, CellName, CellQueryValue, CellTypeStaticInfo } from "./types";
 
+
+/**
+ * 
+ * @todo these functions should be moved out of the celllineage directory and into common probably
+ */
 export const getCellColor = (cell: CellName | CellQueryValue | CellDisplayName): string => {
   return Object.values(cellTypeStaticInfo).find((x: CellTypeStaticInfo) => x.id === cell || x.displayName === cell || extractQueryValues(x, "B").includes(cell as CellQueryValue))?.color ?? "#000000"
 }

diff --git a/immuscreen/src/app/page.tsx b/immuscreen/src/app/page.tsx
@@ -39,7 +39,6 @@ const Home = () => {
             <Select
               id="portal-select"
               value={selectedPortal}
-              // defaultValue={10}
               onChange={handleChange}
             >
               <MenuItem value={"Genes"}>Genes</MenuItem>

diff --git a/immuscreen/src/common/consts.ts b/immuscreen/src/common/consts.ts
@@ -2,7 +2,7 @@
  * @todo the cell info in this file and in celllineage/utils.ts need to be combined
  */
 
-import { CellName, CellTypeStaticInfo } from "../app/celllineage/types"
+import { CellDisplayName, CellName, CellTypeStaticInfo } from "../app/celllineage/types"
 
 export const cellTypeStaticInfo: { [key in CellName]: CellTypeStaticInfo } = {
   Monocytes: {
@@ -529,7 +529,7 @@ export const experimentInfo: { [key: string]: {order: number, description: strin
   '1020-CD34_Cord_Blood-SRX1427814': { order: 1, description: 'CD34+ Cord Blood in donor 1020', displayName: 'CD34+ Cord Blood', group: 'Progenitors', study: 'Corces et al', pmid: '27526324' },
   '7291-CD34_Bone_Marrow-SRX1427812': { order: 2, description: 'CD34+ Bone Marrow in donor 7291', displayName: 'CD34+ Bone Marrow', group: 'Progenitors', study: 'Corces et al', pmid: '27526324' },
   '7292-CD34_Bone_Marrow-SRX1427813': { order: 3, description: 'CD34+ Bone Marrow in donor 7292', displayName: 'CD34+ Bone Marrow', group: 'Progenitors', study: 'Corces et al', pmid: '27526324' },
-  '2596-HSC-SRX1427829': { order: 4, description: 'Hematopoetic Stem Cells in donor 2596', displayName: 'Hematopoetic Stem Cells', group: 'Progenitors', study: 'Corces et al', pmid: '27526324' },
+  '2596-HSC-SRX1427829': { order: 4, description: 'Hematopoetic Stem Cells in donor 2596', displayName: 'Hematopoetic stem ells', group: 'Progenitors', study: 'Corces et al', pmid: '27526324' },
   '2596-HSC-SRX1427830': { order: 5, description: 'Hematopoetic Stem Cells in donor 2596', displayName: 'Hematopoetic Stem Cells', group: 'Progenitors', study: 'Corces et al', pmid: '27526324' },
   '4983-HSC-SRX1427789': { order: 6, description: 'Hematopoetic Stem Cells in donor 4983', displayName: 'Hematopoetic Stem Cells', group: 'Progenitors', study: 'Corces et al', pmid: '27526324' },
   '6792-HSC-SRX1427800': { order: 7, description: 'Hematopoetic Stem Cells in donor 6792', displayName: 'Hematopoetic Stem Cells', group: 'Progenitors', study: 'Corces et al', pmid: '27526324' },

diff --git a/immuscreen/src/common/gbview/bulkatactracks.tsx b/immuscreen/src/common/gbview/bulkatactracks.tsx
@@ -8,7 +8,7 @@ import { client } from "../utils"
 import BulkAtacTrackModal from "./bulkatacmodal";
 import { BulkAtacCelltypeTrack, CalderonCellTypesMetadata } from "./consts";
 import { CellQueryValue } from "../../app/celllineage/types";
-import { getCellDisplayName } from "../../app/celllineage/utils";
+import { getCellColor, getCellDisplayName } from "../../app/celllineage/utils";
 
 export const DEFAULT_TRACKS = (
   assembly: string
@@ -162,6 +162,7 @@ export const TitledTrack: React.FC<{
           //tooltipContent={(rect) => <CCRETooltip {...rect} assembly="grch38" />}
           />
         ) : (
+          // This is the bulk atac
           <FullBigWig
             transform="translate(0,40)"
             width={1400}
@@ -179,10 +180,15 @@ export const TitledTrack: React.FC<{
 
   const BulkAtacTracks: React.FC<BulkAtacTrackProps> = (props: BulkAtacTrackProps) => {
 
-  const defaultTracks: [string, string][] = props.defaultcelltypes?.map((cell: CellQueryValue) => [getCellDisplayName(cell, true, true), `https://downloads.wenglab.org/${cell}.bigWig`]) || []
+  const bulkAtacColors: {[key:string]: string} = {}
+
+  const defaultTracks: [string, string][] = props.defaultcelltypes?.map((cell: CellQueryValue) => {
+    bulkAtacColors[getCellDisplayName(cell, true, true)] = getCellColor(cell)
+    return [getCellDisplayName(cell, true, true), `https://downloads.wenglab.org/${cell}.bigWig`]
+  }) || []
+
   defaultTracks.sort()
   defaultTracks.unshift(["All Immune Cells (Aggregate Signal)", "https://downloads.wenglab.org/all_immune.bigWig"])
-  console.log(defaultTracks)
 
   //Why is this this not working when you have a lot of tracks? Why did my changes matter?
   const [cTracks, setTracks] = useState<[string, string][]>(defaultTracks);
@@ -213,6 +219,7 @@ export const TitledTrack: React.FC<{
     <EmptyTrack width={1400} height={40} transform="" id="" text="Loading..." />
   ) : (
     <>
+    {/* Need to add all cell types to this */}
       <BulkAtacTrackModal
         open={settingsModalShown}
         onCancel={() => setSettingsModalShown(false)}
@@ -235,6 +242,8 @@ export const TitledTrack: React.FC<{
           svgRef={props.svgRef}
           data={data.data}
           transform={`translate(0,${i * 70})`}
+          //Need to add the color here
+          color={bulkAtacColors[cTracks[i][0]]}
         />
       ))}
       <g className="tf-motifs">