Skip to content

Fix: NA groups being omitted from plotly plots #1208

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Swargambharath987 wants to merge 1 commit into
base: devel
Choose a base branch
from
Open

Fix: NA groups being omitted from plotly plots #1208

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 9 additions & 2 deletions www/api/resources/plotly_data.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -302,8 +302,15 @@ def post(self, dataset_id):
dataframe = pd.concat([dataframe,selected.obs], axis=1)

# fill any missing adata.obs values with "NA"
# The below line gives the error - TypeError: Cannot setitem on a Categorical with a new category (NA), set the categories first
#df = df.fillna("NA")
# Categorical columns must have "NA" added as a category before filling
for col in dataframe.select_dtypes(include="category").columns:
if dataframe[col].isna().any():
if "NA" not in dataframe[col].cat.categories:
dataframe[col] = dataframe[col].cat.add_categories("NA")
dataframe[col] = dataframe[col].fillna("NA")
for col in dataframe.select_dtypes(include="object").columns:
if dataframe[col].isna().any():
dataframe[col] = dataframe[col].fillna("NA")

# Valid analysis column names from api/resources/h5ad.py
analysis_tsne_columns = ['X_tsne_1', 'X_tsne_2']
Expand Down