Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-correlations

4 files changed, 94 insertions, 66 deletions

diff --git a/gn3/api/heatmaps.py b/gn3/api/heatmaps.py
index 62ca2ad..633a061 100644
--- a/gn3/api/heatmaps.py
+++ b/gn3/api/heatmaps.py
@@ -17,7 +17,9 @@ def clustered_heatmaps():
     Parses the incoming data and responds with the JSON-serialized plotly figure
     representing the clustered heatmap.
     """
-    traits_names = request.get_json().get("traits_names", tuple())
+    heatmap_request = request.get_json()
+    traits_names = heatmap_request.get("traits_names", tuple())
+    vertical = heatmap_request.get("vertical", False)
     if len(traits_names) < 2:
         return jsonify({
             "message": "You need to provide at least two trait names."
@@ -30,7 +32,7 @@ def clustered_heatmaps():
     traits_fullnames = [parse_trait_fullname(trait) for trait in traits_names]
 
     with io.StringIO() as io_str:
-        _filename, figure = build_heatmap(traits_fullnames, conn)
+        figure = build_heatmap(traits_fullnames, conn, vertical=vertical)
         figure.write_json(io_str)
         fig_json = io_str.getvalue()
     return fig_json, 200
diff --git a/gn3/app.py b/gn3/app.py
index a25332c..3d68b3f 100644
--- a/gn3/app.py
+++ b/gn3/app.py
@@ -21,12 +21,6 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask:
     # Load default configuration
     app.config.from_object("gn3.settings")
 
-    CORS(
-        app,
-        origins=app.config["CORS_ORIGINS"],
-        allow_headers=app.config["CORS_HEADERS"],
-        supports_credentials=True, intercept_exceptions=False)
-
     # Load environment configuration
     if "GN3_CONF" in os.environ:
         app.config.from_envvar('GN3_CONF')
@@ -37,6 +31,13 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask:
             app.config.update(config)
         elif config.endswith(".py"):
             app.config.from_pyfile(config)
+
+    CORS(
+        app,
+        origins=app.config["CORS_ORIGINS"],
+        allow_headers=app.config["CORS_HEADERS"],
+        supports_credentials=True, intercept_exceptions=False)
+
     app.register_blueprint(general, url_prefix="/api/")
     app.register_blueprint(gemma, url_prefix="/api/gemma")
     app.register_blueprint(rqtl, url_prefix="/api/rqtl")
diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py
index 3b94e88..bf9dfd1 100644
--- a/gn3/heatmaps.py
+++ b/gn3/heatmaps.py
@@ -103,7 +103,9 @@ def get_loci_names(
         __get_trait_loci, [v[1] for v in organised.items()], {})
     return tuple(loci_dict[_chr] for _chr in chromosome_names)
 
-def build_heatmap(traits_names, conn: Any):
+def build_heatmap(
+        traits_names: Sequence[str], conn: Any,
+        vertical: bool = False) -> go.Figure:
     """
     heatmap function
 
@@ -155,17 +157,21 @@ def build_heatmap(traits_names, conn: Any):
         zip(traits_ids,
             [traits[idx]["trait_fullname"] for idx in traits_order]))
 
-    return generate_clustered_heatmap(
+    return clustered_heatmap(
         process_traits_data_for_heatmap(
             organised, traits_ids, chromosome_names),
         clustered,
-        "single_heatmap_{}".format(random_string(10)),
-        y_axis=tuple(
-            ordered_traits_names[traits_ids[order]]
-            for order in traits_order),
-        y_label="Traits",
-        x_axis=chromosome_names,
-        x_label="Chromosomes",
+        x_axis={
+            "label": "Chromosomes",
+            "data": chromosome_names
+        },
+        y_axis={
+            "label": "Traits",
+            "data": tuple(
+                ordered_traits_names[traits_ids[order]]
+                for order in traits_order)
+        },
+        vertical=vertical,
         loci_names=get_loci_names(organised, chromosome_names))
 
 def compute_traits_order(slink_data, neworder: tuple = tuple()):
@@ -284,68 +290,81 @@ def process_traits_data_for_heatmap(data, trait_names, chromosome_names):
         for chr_name in chromosome_names]
     return hdata
 
-def generate_clustered_heatmap(
-        data, clustering_data, image_filename_prefix, x_axis=None,
-        x_label: str = "", y_axis=None, y_label: str = "",
+def clustered_heatmap(
+        data: Sequence[Sequence[float]], clustering_data: Sequence[float],
+        x_axis,#: Dict[Union[str, int], Union[str, Sequence[str]]],
+        y_axis: Dict[str, Union[str, Sequence[str]]],
         loci_names: Sequence[Sequence[str]] = tuple(),
-        output_dir: str = TMPDIR,
-        colorscale=((0.0, '#0000FF'), (0.5, '#00FF00'), (1.0, '#FF0000'))):
+        vertical: bool = False,
+        colorscale: Sequence[Sequence[Union[float, str]]] = (
+            (0.0, '#0000FF'), (0.5, '#00FF00'), (1.0, '#FF0000'))) -> go.Figure:
     """
     Generate a dendrogram, and heatmaps for each chromosome, and put them all
     into one plot.
     """
     # pylint: disable=[R0913, R0914]
-    num_cols = 1 + len(x_axis)
+    x_axis_data = x_axis["data"]
+    y_axis_data = y_axis["data"]
+    num_plots = 1 + len(x_axis_data)
     fig = make_subplots(
-        rows=1,
-        cols=num_cols,
-        shared_yaxes="rows",
+        rows=num_plots if vertical else 1,
+        cols=1 if vertical else num_plots,
+        shared_xaxes="columns" if vertical else False,
+        shared_yaxes=False if vertical else "rows",
+        vertical_spacing=0.010,
         horizontal_spacing=0.001,
-        subplot_titles=["distance"] + x_axis,
+        subplot_titles=["" if vertical else x_axis["label"]] + [
+            "Chromosome: {}".format(chromo) if vertical else chromo
+            for chromo in x_axis_data],#+ x_axis_data,
         figure=ff.create_dendrogram(
-            np.array(clustering_data), orientation="right", labels=y_axis))
+            np.array(clustering_data),
+            orientation="bottom" if vertical else "right",
+            labels=y_axis_data))
     hms = [go.Heatmap(
         name=chromo,
-        x=loci,
-        y=y_axis,
+        x=y_axis_data if vertical else loci,
+        y=loci if vertical else y_axis_data,
         z=data_array,
+        transpose=vertical,
         showscale=False)
            for chromo, data_array, loci
-           in zip(x_axis, data, loci_names)]
+           in zip(x_axis_data, data, loci_names)]
     for i, heatmap in enumerate(hms):
-        fig.add_trace(heatmap, row=1, col=(i + 2))
-
-    fig.update_layout(
-        {
-            "width": 1500,
-            "height": 800,
-            "xaxis": {
+        fig.add_trace(
+            heatmap,
+            row=((i + 2) if vertical else 1),
+            col=(1 if vertical else (i + 2)))
+
+    axes_layouts = {
+        "{axis}axis{count}".format(
+            axis=("y" if vertical else "x"),
+            count=(i+1 if i > 0 else "")): {
                 "mirror": False,
-                "showgrid": True,
-                "title": x_label
-            },
-            "yaxis": {
-                "title": y_label
+                "showticklabels": i == 0,
+                "ticks": "outside" if i == 0 else ""
             }
-        })
+        for i in range(num_plots)}
 
-    x_axes_layouts = {
-        "xaxis{}".format(i+1 if i > 0 else ""): {
-            "mirror": False,
-            "showticklabels": i == 0,
-            "ticks": "outside" if i == 0 else ""
-        }
-        for i in range(num_cols)}
+    print("vertical?: {} ==> {}".format("T" if vertical else "F", axes_layouts))
 
-    fig.update_layout(
-        {
-            "width": 4000,
-            "height": 800,
-            "yaxis": {
-                "mirror": False,
-                "ticks": ""
-            },
-            **x_axes_layouts})
+    fig.update_layout({
+        "width": 800 if vertical else 4000,
+        "height": 4000 if vertical else 800,
+        "{}axis".format("x" if vertical else "y"): {
+            "mirror": False,
+            "ticks": "",
+            "side": "top" if vertical else "left",
+            "title": y_axis["label"],
+            "tickangle": 90 if vertical else 0,
+            "ticklabelposition": "outside top" if vertical else "outside left"
+        },
+        "{}axis".format("y" if vertical else "x"): {
+            "mirror": False,
+            "showgrid": True,
+            "title": "Distance",
+            "side": "right" if vertical else "top"
+        },
+        **axes_layouts})
     fig.update_traces(
         showlegend=False,
         colorscale=colorscale,
@@ -353,7 +372,5 @@ def generate_clustered_heatmap(
     fig.update_traces(
         showlegend=True,
         showscale=True,
-        selector={"name": x_axis[-1]})
-    image_filename = "{}/{}.html".format(output_dir, image_filename_prefix)
-    fig.write_html(image_filename)
-    return image_filename, fig
+        selector={"name": x_axis_data[-1]})
+    return fig
diff --git a/gn3/settings.py b/gn3/settings.py
index 150d96d..d5f1d3c 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -35,10 +35,18 @@ GENOTYPE_FILES = os.environ.get(
     "GENOTYPE_FILES", "{}/genotype_files/genotype".format(os.environ.get("HOME")))
 
 # CROSS-ORIGIN SETUP
-CORS_ORIGINS = [
+def parse_env_cors(default):
+    """Parse comma-separated configuration into list of strings."""
+    origins_str = os.environ.get("CORS_ORIGINS", None)
+    if origins_str:
+        return [
+            origin.strip() for origin in origins_str.split(",") if origin != ""]
+    return default
+
+CORS_ORIGINS = parse_env_cors([
     "http://localhost:*",
     "http://127.0.0.1:*"
-]
+])
 
 CORS_HEADERS = [
     "Content-Type",