Initial commit

debbiemarkslab · Jan 26, 2017 · 091fdb6 · 091fdb6
commit 091fdb6
Show file tree

Hide file tree

Showing 10 changed files with 2,358 additions and 0 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,3 @@
+build/
+node_modules/
+**/*.params
diff --git a/README.md b/README.md
@@ -0,0 +1,25 @@
+# EVzoom
+[EVzoom](https://marks.hms.harvard.edu/evzoom/) is an interactive, embeddable tool for visualizing [undirected graphical models](https://en.wikipedia.org/wiki/Markov_random_field) of protein families. Since these models explicitly parameterize all possible combinations of amino acids at all pairs of positions in a sequence, they contain far too much information to depict statically.
+
+EVzoom lets you zoom in on any pair of positions in a protein family and see both inferred couplings between amino acids and [sequence logos](https://en.wikipedia.org/wiki/Sequence_logo) that summarize conservation statistics.
+<p align="center"><img src="https://marks.hms.harvard.edu/evzoom/evzoom.gif" width="500"></p>
+
+EVzoom is based on SVG and powered by [D3](https://d3js.org/).
+
+## Inference
+EVzoom is designed to be used with models inferred by [plmc](https://github.com/debbiemarkslab/plmc). The [examples](https://github.com/debbiemarkslab/plmc#examples) in the plmc repo show how to export JSON-formatted model files for EVzoom.
+
+Want to work directly with the couplings in an EVzoom visualization? Check out the [EVmutation](https://github.com/debbiemarkslab/EVmutation) Python package written by Thomas Hopf.
+
+## Embedding
+Embedding EVzoom takes two lines
+
+```html
+<div id="evzoom-viewer" data-couplings="/data/dhfr.json"> </div>
+<script src="dist/evzoom.js"></script>
+```
+
+The `data-couplings` tag specifies the URL for the json file. This tag can be overridden by appending a query string `?data=JSON_URL` to the URL. An example of the tag-based approach is available in `example/evzoom.html`. To take it for a spin and serve it from your filesystem, run `python -m SimpleHTTPServer 8000` in the root of the repository (requires Python 2.7) and navigate to `localhost:8000/example/evzoom.html` in your browser.
+
+## Author
+EVzoom was written by [John Ingraham](mailto:[email protected]) in [Debora Marks' lab](https://marks.hms.harvard.edu/) at Harvard Medical School
diff --git a/data/dhfr.json b/data/dhfr.json
diff --git a/dist/evzoom.js b/dist/evzoom.js
diff --git a/evzoom.sublime-project b/evzoom.sublime-project
@@ -0,0 +1,15 @@
+{
+	"folders":
+	[
+		{
+			"path": "."
+		}
+	],
+	"build_systems":
+    [
+        {
+            "name": "Build",
+            "shell_cmd": "npm run build"
+        }
+    ]
+}
diff --git a/example/evzoom.html b/example/evzoom.html
@@ -0,0 +1,7 @@
+<!DOCTYPE html>
+<meta charset="utf-8">
+<title>EVzoom</title>
+<center>
+<div id="evzoom-viewer" data-couplings="../data/dhfr.json"> </div>
+<script src="../dist/evzoom.js"></script>
+</center>
diff --git a/package.json b/package.json
@@ -0,0 +1,29 @@
+{
+  "name": "evzoom",
+  "version": "0.1.0",
+  "description": "",
+  "main": "dist/evzoom.js",
+  "scripts": {
+    "build": "rollup -c && uglifyjs build/evzoom.dev.js -cm > dist/evzoom.js"
+  },
+  "homepage": "https://github.com/debbiemarkslab/EVzoom",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/debbiemarkslab/EVzoom.git"
+  },
+  "bugs": {
+    "url": "https://github.com/debbiemarkslab/EVzoom/issues"
+  },
+  "author": "John Ingraham <[email protected]>",
+  "contributors": [],
+  "license": "",
+  "keywords": [
+    "Coevolution",
+    "Undirected graphical model"
+  ],
+  "devDependencies": {
+    "d3": "^4.0.0",
+    "rollup-plugin-node-resolve": "^2.0.0"
+  },
+  "dependencies": {}
+}
diff --git a/rollup.config.js b/rollup.config.js
@@ -0,0 +1,9 @@
+import npm from "rollup-plugin-node-resolve";
+
+export default {
+  entry: "src/evzoom.js",
+  dest: "build/evzoom.dev.js",
+  format: "umd",
+  moduleName: "d3",
+  plugins: [npm({jsnext: true})]
+};
diff --git a/src/README.md b/src/README.md
@@ -0,0 +1,17 @@
+
+# Compiling EVzoom
+Note: The following is only required for development. A compiled, ready-to-run version of EVzoom is provided at dist/evzoom.js.
+
+## Install dependencies
+EVzoom is bundled and minified with the Node.js packages `rollup` and `uglifyjs`. After installing Node, these dependencies can be globally installed with
+
+    npm install -g rollup
+    npm install -g uglify-js
+
+## Building
+To build EVzoom, run
+
+    npm install
+    npm run build
+
+This will build evzoom into dist/evzoom.js.