Modules Not Visible After Running `findModules()`

[victorsanchezarevalo]

I am here again! Sorry to bother you but I use your package a lot!!

Description:

After running the following sequence of WGCNA commands, the modules are not visible:

wgcna.preprocess()

# Find Modules
wgcna.findModules()

# Add color for metadata
wgcna.setMetadataColor('treatment', {'TPA': 'green',
                                    'acetone': 'yellow'})
wgcna.setMetadataColor('condition', {'WT': 'darkviolet',
                                    'KO': 'deeppink'})
wgcna.setMetadataColor('time', {'day_2': 'plum',
                                'day_4': 'violet',
                                'day_6': 'purple',
                                'day_8': 'red'})

# Analyse WGCNA and save results
wgcna.analyseWGCNA()
wgcna.saveWGCNA()

Despite successfully running the commands without errors, I cannot see the modules that were supposed to be generated during the findModules() step.

Expected Behavior:

• Modules should be updated.

Observed Behavior:

• Modules are not updated.

Additional Information:

• No errors were observed in the console/logs during the execution.
• Metadata colors were added successfully.

Let me know if you need further details to reproduce the issue. Thank you for your assistance!

[nargesr]

Hi,

Sorry, I didn't catch the problem completely! It didn't produce any error but no plot was generated as well??

Can you also send me the full script you used (including how you initiated the object) along with the complete output?