Seeking help on `order` Parameter Usage and Metadata Color Settings about pywgcna HOT 13 CLOSED

Hi,
Thank you for your kind comments:)

1. you need to specify this when you update your metadata. but I just realized I updated it in a way you don’t need to specify it. the only key import thing is that the index should match and it will update it based on the index
   for more information look at the updateGeneInfo() and updateSampleInfo().

I will update the Data_format in the next week to reflect changes (I will notify you through this issue).

thanks for catching this :)

2. if you have a continuous value you can pass the color as a color palette using matplotlib.cm.ScalarMappable.

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Hi @nargesr , thanks so much for your time and kind help. Now everything works well in the new version.

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Thanks for your quick reply. Sorry, I may still have a naive question😂. Regarding the second solution, I attempted the following codes, but encountered an error: AttributeError: 'ScalarMappable' object has no attribute 'keys'.

import matplotlib as mpl
norm = mpl.colors.Normalize(vmin=min(adata.obs['age']), 
                            vmax=max(adata.obs['age']))
cmap = mpl.colormaps['viridis']
pyWGCNA.setMetadataColor('age', mpl.cm.ScalarMappable(norm, cmap))

pyWGCNA.analyseWGCNA(geneList=adata.var)

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Hi @KGZaker,

I believe I used the same script! lol
can you send me the full error?

import matplotlib as mpl

norm = mpl.colors.Normalize(vmin=adata.obs['age'].min(), 
                            vmax=adata.obs['age'].max())
my_palette_age = mpl.cm.ScalarMappable(norm=norm, cmap='viridis')

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Hi, thanks for helping me figure out what's wrong. Here is the code I used and errors I got:

pyWGCNA.updateSampleInfo(adata.obs[["sex", "age"]])

norm = mpl.colors.Normalize(vmin=adata.obs['age'].min(),  vmax=adata.obs['age'].max())
my_palette_age = mpl.cm.ScalarMappable(norm=norm, cmap='viridis')

pyWGCNA.setMetadataColor('age', my_palette_age)
pyWGCNA.barplotModuleEigenGene(moduleName="white", metadata=["age"])

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[229], line 1
----> 1 pyWGCNA.barplotModuleEigenGene(moduleName="white", metadata=["age"])

File [~/micromamba/envs/macbiom/lib/python3.11/site-packages/PyWGCNA/wgcna.py:3028](http://localhost:8889/~/micromamba/envs/macbiom/lib/python3.11/site-packages/PyWGCNA/wgcna.py#line=3027), in WGCNA.barplotModuleEigenGene(self, moduleName, metadata, combine, colorBar, show)
   3026 height_ratios = []
   3027 for m in metadata:
-> 3028     height_ratios.append(len(list(self.metadataColors[m].keys())))
   3029 height_ratios.reverse()
   3031 modules = np.unique(self.datExpr.var['moduleColors']).tolist()

AttributeError: 'ScalarMappable' object has no attribute 'keys'

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Hi @KGZaker

I just released the new version (2.0.4) which hopefully will solve your problem. Please upgrade the PyWGCNA and let me know if you still have the same problem

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