From a6142bdf93e4acffd687decb398fd553df39a5f9 Mon Sep 17 00:00:00 2001
From: Bruce Martin <bruce@chanzuckerberg.com>
Date: Thu, 30 May 2019 13:31:41 -0700
Subject: [PATCH] improve graph scale and centering (#796)

* add gutter to embedding canvas

* improve layout scale and translate

* fix lint

* pin tables to version 3.5.1

* fix lasso coordinate smoke tests
---
 client/__tests__/e2e/data.js              |  6 +++---
 client/src/components/graph/graph.js      |  5 +++--
 server/app/scanpy_engine/scanpy_engine.py | 15 ++++++++++++++-
 server/requirements.txt                   |  2 +-
 4 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/client/__tests__/e2e/data.js b/client/__tests__/e2e/data.js
index 3d48e52e..1b81a3c8 100644
--- a/client/__tests__/e2e/data.js
+++ b/client/__tests__/e2e/data.js
@@ -27,7 +27,7 @@ export const datasets = {
       lasso: [
         {
           "coordinates-as-percent": { x1: 0.05, y1: 0.25, x2: 0.15, y2: 0.35 },
-          count: "104"
+          count: "101"
         }
       ],
       categorical: [
@@ -91,8 +91,8 @@ export const datasets = {
         }
       },
       lasso: {
-        "coordinates-as-percent": { x1: 0.45, y1: 0.05, x2: 0.5, y2: 0.1 },
-        count: "76"
+        "coordinates-as-percent": { x1: 0.45, y1: 0.05, x2: 0.65, y2: 0.15 },
+        count: "46"
       }
     },
     scatter: {
diff --git a/client/src/components/graph/graph.js b/client/src/components/graph/graph.js
index 32a10603..c49063f9 100644
--- a/client/src/components/graph/graph.js
+++ b/client/src/components/graph/graph.js
@@ -146,9 +146,10 @@ class Graph extends React.Component {
     const sizeBuffer = regl.buffer();
 
     // preallocate coordinate system transformation between data and gl
+    const fractionToUse = 0.98; // fraction of dimension to use
     const transform = {
-      glScaleX: scaleLinear([0, 1], [-1, 1]),
-      glScaleY: scaleLinear([0, 1], [1, -1])
+      glScaleX: scaleLinear([0, 1], [-1 * fractionToUse, 1 * fractionToUse]),
+      glScaleY: scaleLinear([0, 1], [1 * fractionToUse, -1 * fractionToUse])
     };
 
     /* first time, but this duplicates above function, should be possile to avoid this */
diff --git a/server/app/scanpy_engine/scanpy_engine.py b/server/app/scanpy_engine/scanpy_engine.py
index f1439264..31cb3707 100644
--- a/server/app/scanpy_engine/scanpy_engine.py
+++ b/server/app/scanpy_engine/scanpy_engine.py
@@ -442,13 +442,26 @@ class ScanpyEngine(CXGDriver):
         Caveats:
         * does not support filtering
         * only returns Matrix in columnar layout
+
+        All embeddings must be individually centered & scaled (isotropically)
+        to a [0, 1] range.
         """
         try:
             layout_data = []
             for layout in self.config["layout"]:
                 full_embedding = self.data.obsm[f"X_{layout}"]
                 embedding = full_embedding[:, :2]
-                normalized_layout = (embedding - embedding.min()) / (embedding.max() - embedding.min())
+
+                # scale isotropically
+                min = embedding.min(axis=0)
+                max = embedding.max(axis=0)
+                scale = np.amax(max - min)
+                normalized_layout = (embedding - min) / scale
+
+                # translate to center on both axis
+                translate = 0.5 - ((max - min) / scale / 2)
+                normalized_layout = normalized_layout + translate
+
                 normalized_layout = normalized_layout.astype(dtype=np.float32)
                 layout_data.append(pandas.DataFrame(normalized_layout, columns=[f"{layout}_0", f"{layout}_1"]))
 
diff --git a/server/requirements.txt b/server/requirements.txt
index 0d2a8baa..18ff0f31 100644
--- a/server/requirements.txt
+++ b/server/requirements.txt
@@ -12,4 +12,4 @@ pandas>=0.23.1
 scanpy>=1.3.7
 scipy>=1.1.0
 scikit-learn>=0.19.1,!=0.20.0
-tables>=3.5.1
+tables==3.5.1