Merge pull request #6 from thomcsmits/thomcsmits/gh

add readme/license/fix demo's

LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Thomas C. Smits
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# CellPop: Cell Type Composition Explorer
+CellPop is a visualization tool for cell type compositions. It is an NPM package that exports various functions and to create a D3 visualization from various file types.
+
+
+## Why CellPop? 
+Cell type populations are commonly shown with stacked bar charts. However, scaling the number of samples and cell types in these visualizations create issues with analyzing these charts. CellPop alleviates this by presenting a flexible heatmap and side views with extending layered bar charts.
+
+## How to run
+This project uses pnpm. 
+
+Install dependencies with:
+```sh
+pnpm install
+```
+
+Run the demo with:
+```sh
+pnpm run dev
+```
+
+## Demo
+The demo folder contains three demo's: 
+- The combination of index.jsx and demo.jsx are a React demo, using the HuBMAP data loaders and CellPopComponent, which includes the option bar.
+- Main.js is a JavaScript only demo that uses the HuBMAP data loaders and the mainVis function to create the visualization. 
+- Animation.js shows an animation of how a stacked bar chart converts to the CellPop view.
+
+
+The React demo is available (here)[thomcsmits.github.io/cellpop].
+
+The main view and interactions:
+![Screen shot of cell pop with 29 samples and arrows explaining interactions.](assets/cellpop_example.png)
+
+## Team
+[HiDIVE Lab](https://hidivelab.org)
+- Thomas C. Smits (<[email protected]>)
+- Nils Gehlenborg (<[email protected]>)

demo/animation.js

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+import * as d3 from "d3";
+import { showAnimation } from "../src/visualization/animation";
+import { loadHuBMAPData } from "../src/dataLoading/dataHuBMAP"; 
+// data
+var uuids = ['ad693f99fb9006e68a53e97598da1509',
+    '173de2e80adf6a73ac8cff5ccce20dfc',
+	'b95f34761c252ebbd1e482cd9afae73f',
+	'5a5ca03fa623602d9a859224aa40ace4',
+	'3c1b10bc912c60c9afc36b7423695236',
+	'1dc16eb0270ff73291dd45b6a96aa3c0',
+	'b05c21f9c94ce1a22a9694cd0fe0291e',
+	'8cdb42ed1194255c74c8462b99bbd7ef',
+	'fe0ded5fc0355c95239f9c040dd31e99',
+	'367fee3b40cba682063289505b922be1',
+	'b99fc30c4195958fbef217fa9ed9ec8f',
+	'898138b7f45a67c574e9955fb400e9be',
+	'f220c9e7bcaea3a87162cbe61287ea4d',
+	'e5f7a14d93659bd0b8dc2819ffa9bc4b',
+	'56cbda4789f04d79c0c3dffe21816d48',
+	'0b6f63f2bd61a8c091fc7afc0f318ad1',
+	'62efbe0a6abd0bcf53ab9ab29e7cd73f',
+	'4b62d9d2c248323ce029859f953fdc57',
+	'c81b0dc9d16eb825a7d6bce6e1b3678f',
+	'5ee240959c96b49d960702755478b9fc',
+	'7c9e07c96d144536525b1f889acee14d',
+	'dd7ccbc306692fc5ff5e61c22845da21',
+	'9a7e6be288b27ddbd3366c4ae41bbcd2',
+	'018a905cdbdff684760859f594d3fd77',
+	'af5741dad7aecf7960a129c3d2ae642a',
+	'6e1db473492095ccc2f1393d7259b9c0',
+	'fae9a1f2e7abefca2203765a3c7a5ba1',
+	'8d631eee88855ac59155edca2a3bc1ca',
+	'1ea6c0ac5ba60fe35bf63af8699b6fbe']
+
+
+// Load data directly as demo
+loadHuBMAPData(uuids).then((data) => {
+	showAnimation(data);
+}).catch(error => {
+	console.error(error);
+});

demo/main.js

@@ -1,7 +1,7 @@
 import * as d3 from "d3";
-import { getMainVis } from "./src/visualization";
-import { showAnimation } from "./src/visualization/animation";
-import { loadHuBMAPData } from "./src/dataLoading/dataHuBMAP"; 
+import { getMainVis } from "../src/visualization";
+import { showAnimation } from "../src/visualization/animation";
+import { loadHuBMAPData } from "../src/dataLoading/dataHuBMAP"; 
 
 // data
 var uuids = ['ad693f99fb9006e68a53e97598da1509',