Skip to content

Edge case handling in barplotModuleEigenGene color palettes #148

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
mattjmeier wants to merge 1 commit into
base: main
Choose a base branch
from
+22 −4
Open

Edge case handling in barplotModuleEigenGene color palettes #148

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
26 changes: 22 additions & 4 deletions PyWGCNA/wgcna.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3129,10 +3129,28 @@ def barplotModuleEigenGene(self, moduleName, metadata, combine=True, colorBar=No
palette.replace(self.metadataColors[colorBar], inplace=True)
palette = palette[colorBar].values
else:
palette = cat[[colorBar]].copy()
palette[[colorBar]] = palette[[colorBar]].astype('int')
palette[colorBar] = palette[colorBar].apply(lambda x: mcolors.to_hex(self.metadataColors[colorBar].to_rgba(float(x))) if pd.notna(x) else "#FFFFFF")
palette = palette[colorBar].values
palette_df = cat[[colorBar]].copy()

# Get the color mapping dictionary for the current trait (e.g., 'chemical')
color_map = self.metadataColors[colorBar]

# Check if the mapping is a dictionary (for categorical data)
if isinstance(color_map, dict):
# Directly map the category names to their hex color codes.
# This is where a string like 'nan' would fail to map, resulting in a np.nan value.
palette_df[colorBar] = palette_df[colorBar].map(color_map)

# Fill any unmapped values (which become np.nan) with a default color.
palette_df[colorBar].fillna("#D3D3D3", inplace=True) # Use light gray for missing/unmapped data

else:
# This retains the new logic for when the color_map is a colormap object (for numeric data)
# We should add similar protection here.
palette_df[colorBar] = palette_df[colorBar].apply(
lambda x: mcolors.to_hex(color_map.to_rgba(float(x))) if pd.notna(x) and str(x).lower() != 'nan' else "#D3D3D3"
)

palette = palette_df[colorBar].values

fig, axs = plt.subplots(nrows=2, ncols=2, figsize=(cat.shape[0] + 2, len(metadata) * 4),
sharex='col', gridspec_kw={
Expand Down