fix ReferenceError; updated README and movie

Author: Benedikt Obermayer

HISTORY.rst

@@ -2,6 +2,13 @@
 History
 =======
 
+------
+v0.7.2
+------
+
+- fix ReferenceError
+- updated README and tutorialmovie
+
 ------
 v0.7.1
 ------

README.rst

@@ -237,6 +237,7 @@ The prerequisites are:
 - Python 3, either
     - system-wide installation with ``virtualenv``, or
     - installed with `Conda <https://docs.conda.io/en/latest/>`__.
+- `Git LFS <https://git-lfs.github.com/>`__ must be installed for obtaining the example data files.
 
 For ``virtualenv``, first create a virtual environment and activate it.
 
@@ -254,6 +255,7 @@ For a Conda-based setup create a new environment and activate it.
 
 Next, clone the repository and install the software as editable (``-e``).
 Also install the development requirements to get helpers such as black.
+(Note that you must have `Git LFS <https://git-lfs.github.com/>`__ installed to actually obtain the data files).
 
 .. code-block:: shell
 

scelvis/ui/cells.py

@@ -47,6 +47,8 @@ def render_controls_scatter(data):
                 ),
                 html.Hr(),
                 render_select_cells(data),
+                # hidden div to store selection of cells
+                html.Div(id="select_cells_selected", style={"display": "none"}),
             ],
             title="Select x- and y-coordinates for embedding (TSNE or UMAP); "
             "color points according to cell annotation (e.g., cluster identity or n_genes); "
@@ -189,10 +191,10 @@ def render_select_cells_controls(data):
                         id="select_cells_view_groups",
                         color="link",
                         style={
-                            "padding-left": 2,
-                            "padding-right": 2,
-                            "padding-top": 0,
-                            "padding-bottom": 3,
+                            "paddingLeft": 2,
+                            "paddingRight": 2,
+                            "paddingTop": 0,
+                            "paddingBottom": 3,
                         },
                     ),
                     "or",
@@ -201,10 +203,10 @@ def render_select_cells_controls(data):
                         id="select_cells_view_table",
                         color="link",
                         style={
-                            "padding-left": 2,
-                            "padding-right": 0,
-                            "padding-top": 0,
-                            "padding-bottom": 3,
+                            "paddingLeft": 2,
+                            "paddingRight": 0,
+                            "paddingTop": 0,
+                            "paddingBottom": 3,
                         },
                     ),
                     "; download ",
@@ -227,7 +229,6 @@ def render_select_cells_controls(data):
                 id="select_cells_get_results",
                 style={"display": "none"},
             ),
-            html.Div(id="select_cells_results", style={"display": "none"}),
         ]
     )
 
@@ -263,19 +264,18 @@ def render_controls(data):
         html.Hr(),
         # Placeholder for the plot-specific controls.
         html.Div(id="meta_plot_controls"),
+        # hidden div for selection results
+        html.Div(id="select_cells_results", style={"display": "none"}),
     ]
 
 
 def render(data):
     """Render the "Cell Annotation" content."""
     return dbc.Row(
         children=[
-            # hidden div to store selection of cells
-            html.Div(id="select_cells_selected", style={"display": "none"}),
             dbc.Col(children=render_controls(data), className="col-3"),
             # Placeholder for the plot.
             dbc.Col(children=[dcc.Loading(id="meta_plot", type="circle")], className="col-9"),
-            # dbc.Col(children=[html.Div(id="meta_plot")], className="col-9"),
         ]
     )
 
@@ -302,8 +302,12 @@ def render_plot_scatter(data, xc, yc, col, filters_json, select_json):
                 return {}, "", True
 
             # make sure groups are disjoint
-            group_A = list(set(selected["group_A"]) - set(selected["group_B"]))
-            group_B = list(set(selected["group_B"]) - set(selected["group_A"]))
+            group_A = list(
+                (set(selected["group_A"]) - set(selected["group_B"])) & set(ad_here.obs_names)
+            )
+            group_B = list(
+                (set(selected["group_B"]) - set(selected["group_A"])) & set(ad_here.obs_names)
+            )
 
             if len(group_A) == 0 or len(group_B) == 0:
                 return {}, "", True

scelvis/ui/common.py

@@ -35,37 +35,43 @@ def render_plot(data_type, plot_type):
 
 def render_filter_cells_collapse(data, token):
 
-    return html.Div(
-        [
-            dbc.Button(
-                "filter cells",
-                id="%s_filter_cells_button" % token,
-                className="text-left",
-                color="primary",
-                outline=True,
-                size="md",
-            ),
-            dbc.Collapse(
-                dbc.Card(dbc.CardBody(render_filter_cells_controls(data, token))),
-                id="%s_filter_cells_collapse" % token,
-            ),
-        ],
-        id="%s_filter_cells_div" % token,
-    )
+    children = [
+        dbc.Button(
+            "filter cells",
+            id="%s_filter_cells_button" % token,
+            className="text-left",
+            color="primary",
+            outline=True,
+            size="md",
+        ),
+        dbc.Collapse(
+            dbc.Card(dbc.CardBody(render_filter_cells_controls(data, token))),
+            id="%s_filter_cells_collapse" % token,
+        ),
+    ]
+
+    if token == "meta":
+        # store list of choices in hidden div
+        filters = {}
+        children.append(
+            html.Div(
+                id="filter_cells_filters", style={"display": "none"}, children=json.dumps(filters)
+            )
+        )
+
+    return html.Div(children=children, id="%s_filter_cells_div" % token)
 
 
 def render_filter_cells_controls(data, token):
 
-    # store list of choices in hidden div
-    filters = {}
     options = (
         [{"label": "ncells", "value": "ncells"}]
         + [{"label": c, "value": c} for c in data.categorical_meta]
         + [{"label": c, "value": c} for c in data.numerical_meta]
         + [{"label": g, "value": g} for g in data.genes]
     )
 
-    output = [
+    return [
         html.Div(
             [dcc.Dropdown(id="%s_filter_cells_attribute" % token, options=options, value="None")]
         ),
@@ -135,15 +141,6 @@ def render_filter_cells_controls(data, token):
         ),
     ]
 
-    if token == "meta":
-        output.append(
-            html.Div(
-                id="filter_cells_filters", style={"display": "none"}, children=json.dumps(filters)
-            )
-        )
-
-    return output
-
 
 def apply_filter_cells_filters(data, filters_json):
 

scelvis/ui/genes.py

@@ -166,7 +166,6 @@ def render(data):
                     # Placeholder for the plot.
                     dbc.Col(
                         children=[dcc.Loading(id="expression_plot", type="circle")],
-                        # children=[html.Div(id="expression_plot")],
                         className="col-9",
                     ),
                 ]