From 16f93397ae2bec221aecca1de61c015c1dec5d48 Mon Sep 17 00:00:00 2001
From: Sidney Bell <sidneymbell@users.noreply.github.com>
Date: Thu, 21 Mar 2019 19:06:05 -0700
Subject: [PATCH] Support `diffmap` and `phate` layouts. Explicitly handle
 embeddings with >2 components. (#662)

* Add diffmap and phate to supported embeddings

* Explicitly pull the first two components of any given layout
---
 README.md                                 | 2 +-
 server/app/scanpy_engine/scanpy_engine.py | 7 ++++++-
 server/cli/launch.py                      | 2 +-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 59559f4a..20473131 100644
--- a/README.md
+++ b/README.md
@@ -37,7 +37,7 @@ You should see your web browser open with the following
 
 There are several options available, such as:
 
-- `--layout` to specify the layout as `tsne`, `umap`, `draw_graph_fa`, or `draw_graph_fr` 
+- `--layout` to specify the layout as `tsne`, `umap`, `diffmap`, `phate`, `draw_graph_fa`, or `draw_graph_fr`
 - `--title` to show a title on the explorer
 - `--open` to automatically open the web browser after launching (OS X only)
 
diff --git a/server/app/scanpy_engine/scanpy_engine.py b/server/app/scanpy_engine/scanpy_engine.py
index 3f54c9b9..88b6bf29 100644
--- a/server/app/scanpy_engine/scanpy_engine.py
+++ b/server/app/scanpy_engine/scanpy_engine.py
@@ -328,10 +328,15 @@ class ScanpyEngine(CXGDriver):
         * only returns Matrix in columnar layout
         """
         try:
-            df_layout = self.data.obsm[f"X_{self.layout_method}"]
+            full_embedding = self.data.obsm[f"X_{self.layout_method}"]
+            if full_embedding.shape[1] > 2:
+                warnings.warn(f"Warning: found {full_embedding.shape[1]} \
+                components of embedding. Using the first two for layout display.")
+            df_layout = full_embedding[:, :2]
         except ValueError as e:
             raise PrepareError(
                 f"Layout has not been calculated using {self.layout_method}, "
                 f"please prepare your datafile and relaunch cellxgene") from e
+
         normalized_layout = (df_layout - df_layout.min()) / (df_layout.max() - df_layout.min())
         return encode_matrix_fbs(normalized_layout.astype(dtype=np.float32), col_idx=None, row_idx=None)
diff --git a/server/cli/launch.py b/server/cli/launch.py
index 6d643bc9..06801388 100644
--- a/server/cli/launch.py
+++ b/server/cli/launch.py
@@ -16,7 +16,7 @@ from server.app.util.utils import custom_format_warning
 @click.option(
     "--layout",
     "-l",
-    type=click.Choice(["umap", "tsne", "draw_graph_fa", "draw_graph_fr"]),
+    type=click.Choice(["umap", "tsne", "draw_graph_fa", "draw_graph_fr", "diffmap", "phate"]),
     default="umap",
     show_default=True,
     help="Method for layout."