[plot] Add plot.html

tanghaibao · Jul 7, 2018 · a1cafed · a1cafed
1 parent efc52af
commit a1cafed
Show file tree

Hide file tree

Showing 2 changed files with 128 additions and 0 deletions.
diff --git a/README.md b/README.md
@@ -86,4 +86,11 @@ allhic build T4_Chr/{prunning.sub.tour,seq.fasta}
 ## WIP features
 
 - [x] Add restriction enzyme for better normalization of contig lengths
+- [ ] Translate "prune" from C++ code to golang
+- [ ] Add partition split inside "partition"
+- [ ] Isolate matrix generation to "plot"
+- [ ] Add "pipeline" to simplify execution
+- [ ] Use clustering when k = 1
+- [ ] Compare numerical output with Lachesis
+- [ ] Improve Ler0 results
 - [ ] Add test suites
diff --git a/plot.html b/plot.html
@@ -0,0 +1,121 @@
+<html>
+    <script src="https://d3js.org/d3.v5.min.js"></script>
+    <script>
+
+// Borrowed from gist: https://gist.github.com/nvictus/88b3b5bfe587d32ac1ab519fd0009607
+// Client-side parser for .npy files
+// See the specification: http://docs.scipy.org/doc/numpy-dev/neps/npy-format.html
+var NumpyLoader = (function () {
+    function asciiDecode(buf) {
+        return String.fromCharCode.apply(null, new Uint8Array(buf));
+    }
+
+    function readUint16LE(buffer) {
+        var view = new DataView(buffer);
+        var val = view.getUint8(0);
+        val |= view.getUint8(1) << 8;
+        return val;
+    }
+
+    function fromArrayBuffer(buf) {
+      // Check the magic number
+      var magic = asciiDecode(buf.slice(0,6));
+      if (magic.slice(1,6) != 'NUMPY') {
+          throw new Error('unknown file type');
+      }
+
+      var version = new Uint8Array(buf.slice(6,8)),
+          headerLength = readUint16LE(buf.slice(8,10)),
+          headerStr = asciiDecode(buf.slice(10, 10+headerLength));
+          offsetBytes = 10 + headerLength;
+          //rest = buf.slice(10+headerLength);  XXX -- This makes a copy!!! https://www.khronos.org/registry/typedarray/specs/latest/#5
+
+      // Hacky conversion of dict literal string to JS Object
+      eval("var info = " + headerStr.toLowerCase().replace('(','[').replace('),',']'));
+
+      // Intepret the bytes according to the specified dtype
+      var data;
+      if (info.descr === "|u1") {
+          data = new Uint8Array(buf, offsetBytes);
+      } else if (info.descr === "|i1") {
+          data = new Int8Array(buf, offsetBytes);
+      } else if (info.descr === "<u2") {
+          data = new Uint16Array(buf, offsetBytes);
+      } else if (info.descr === "<i2") {
+          data = new Int16Array(buf, offsetBytes);
+      } else if (info.descr === "<u4") {
+          data = new Uint32Array(buf, offsetBytes);
+      } else if (info.descr === "<i4") {
+          data = new Int32Array(buf, offsetBytes);
+      } else if (info.descr === "<f4") {
+          data = new Float32Array(buf, offsetBytes);
+      } else if (info.descr === "<f8") {
+          data = new Float64Array(buf, offsetBytes);
+      } else {
+          throw new Error('unknown numeric dtype')
+      }
+
+      return {
+          shape: info.shape,
+          fortran_order: info.fortran_order,
+          data: data
+      };
+    }
+
+    function open(file, callback) {
+        var reader = new FileReader();
+        reader.onload = function() {
+            // the file contents have been read as an array buffer
+            var buf = reader.result;
+            var ndarray = fromArrayBuffer(buf);
+            callback(ndarray);
+        };
+        reader.readAsArrayBuffer(file);
+    }
+
+    function ajax(url, callback) {
+        var xhr = new XMLHttpRequest();
+        xhr.onload = function(e) {
+            var buf = xhr.response; // not responseText
+            var ndarray = fromArrayBuffer(buf);
+            callback(ndarray);
+        };
+        xhr.open("GET", url, true);
+        xhr.responseType = "arraybuffer";
+        xhr.send(null);
+    }
+
+    return {
+        open: open,
+        ajax: ajax
+    };
+})();
+
+function openFile(filename) {
+    var content
+    if (filename.endsWith(".json")) {
+        return fetch(filename)
+            .then(response => response.json());
+    } else {
+        return fetch(filename)
+            .then(response => response.blob());
+    }
+};
+
+async function main() {
+    let genome = await openFile("genome.json");
+    let blob = await openFile("data.npy");
+    let data = NumpyLoader.open(blob, array => array)
+    console.log(genome);
+    console.log(data);
+};
+
+    </script>
+    <head>
+    </head>
+    <body>
+<button onclick="main()">
+Plot
+</button>
+    </body>
+</html>