bug fixes in cell filtering

bihealth · Sep 20, 2021 · 96a3667 · 96a3667
1 parent 1677836
commit 96a3667
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Showing 5 changed files with 27 additions and 15 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,6 +2,12 @@
 History
 =======
 
+------
+v0.8.6
+------
+
+- bug fixes for cell filtering
+
 ------
 v0.8.5
 ------

diff --git a/requirements/notesting.txt b/requirements/notesting.txt
@@ -1,7 +1,7 @@
 # Base requirements
 
 # botocore and pyOpenSSL to avoid incompatibility errors
-botocore
+botocore==1.20.106
 pyOpenSSL
 
 # Dash and friends.
@@ -38,8 +38,9 @@ requests
 htmllistparse
 # TODO: we need an fs[._]irods
 # Access to files through iRODS.
-python-irodsclient
+python-irodsclient >= 1.0.0
 
 # Documentation
 sphinx
 sphinx-rtd-theme
+docutils < 0.17
diff --git a/scelvis/callbacks.py b/scelvis/callbacks.py
@@ -13,6 +13,7 @@
 import dash_html_components as html
 from dash.dependencies import Input, Output, State
 import pandas as pd
+import numpy as np
 from logzero import logger
 from werkzeug.utils import secure_filename
 
@@ -606,6 +607,7 @@ def update_filter_cells_controls(
                 + hidden_rangeslider
             )
 
+        attribute = None
         if ctx.triggered and "meta" in ctx.triggered[0]["prop_id"]:
             token = "meta"
             attribute = meta_attribute
@@ -661,8 +663,12 @@ def update_filter_cells_controls(
                     + hidden_rangeslider
                 )
             else:
-                range_min = values.dropna().min()
-                range_max = values.dropna().max()
+                if np.any(np.isnan(values)):
+                    range_min = values.dropna().min()
+                    range_max = values.dropna().max()
+                else:
+                    range_min = values.min()
+                    range_max = values.max()
                 if attribute in filters:
                     val_min = filters[attribute][0]
                     val_max = filters[attribute][1]

diff --git a/scelvis/convert.py b/scelvis/convert.py
@@ -320,15 +320,11 @@ def _load_expression(self, coords, annotation, markers):
                 "cannot find expression data at %s or %s" % (expression_tsv, expression_mtx)
             )
         logger.info("Combining data")
-        ad = sc.AnnData(
-            X=X,
-            obs=annotation.loc[cells],
-            var=pd.DataFrame([], index=genes),
-        )
-        coords_types = set([re.sub('[-_][0-9]*$','',c).upper() for c in coords.columns])
+        ad = sc.AnnData(X=X, obs=annotation.loc[cells], var=pd.DataFrame([], index=genes))
+        coords_types = set([re.sub("[-_][0-9]*$", "", c).upper() for c in coords.columns])
         for ct in coords_types:
             ct_cols = [c for c in coords.columns if ct in c.upper()]
-            ad.obsm['X_'+ct] = coords.loc[cells, ct_cols].values
+            ad.obsm["X_" + ct] = coords.loc[cells, ct_cols].values
         for col in markers.columns:
             ad.uns["marker_" + col] = markers[col].values
 

diff --git a/scelvis/ui/common.py b/scelvis/ui/common.py
@@ -198,10 +198,13 @@ def auto_tick(data_range, max_tick=10, tf_inside=False):
             tick_size_nmlz = list_tick_size_nmlz[i - 1]
             break
     tick_size = tick_size_nmlz * scale  # tick sizse for the original data
-    ticks = (
-        np.unique(np.arange(data_range[0] / tick_size, data_range[1] / tick_size).round())
-        * tick_size
-    )  # list of ticks
+    if tick_size > 0:
+        ticks = (
+            np.unique(np.arange(data_range[0] / tick_size, data_range[1] / tick_size).round())
+            * tick_size
+        )  # list of ticks
+    else:
+        ticks = data_range[0].round()
 
     if tf_inside:  # if only allow ticks within the given range
         ticks = ticks[(ticks >= data_range[0]) * (ticks <= data_range[1])]