AttributeError: 'NoneType' object has no attribute 'render' about pywgcna HOT 6 CLOSED

I encountered the same problem and found the solution here:
WestHealth/pyvis#223

from pywgcna.

Hi,

would you mind sending the full error?

from pywgcna.

/Users/mksingh/PyWGCNA/figures/network/all.html
Traceback (most recent call last):
File "/Users/mksingh/PyWGCNA/network.py", line 10, in
pyWGCNA_m1_10x.CoexpressionModulePlot(modules=modules, numGenes=10, numConnections=100, minTOM=0, file_name="all")
File "/Users/mksingh/anaconda3/lib/python3.10/site-packages/PyWGCNA/wgcna.py", line 3391, in CoexpressionModulePlot
net.show(f"{self.outputPath}/figures/network/{file_name}.html")
File "/Users/mksingh/anaconda3/lib/python3.10/site-packages/pyvis/network.py", line 546, in show
self.write_html(name, open_browser=False,notebook=True)
File "/Users/mksingh/anaconda3/lib/python3.10/site-packages/pyvis/network.py", line 515, in write_html
self.html = self.generate_html(notebook=notebook)
File "/Users/mksingh/anaconda3/lib/python3.10/site-packages/pyvis/network.py", line 479, in generate_html
self.html = template.render(height=height,
AttributeError: 'NoneType' object has no attribute 'render'

from pywgcna.

can you send me your pickle file?

from pywgcna.

I am attaching all the input files as pickle file is large in size.
sample_info.csv
trimmed_means_transposed.csv

Running script:

import PyWGCNA

geneExp = 'trimmed_means_transposed.csv'

pyWGCNA_m1_10x = PyWGCNA.WGCNA(name='m1_10x', species='human', geneExpPath=geneExp, outputPath='/Users/manojkumarsingh/PyWGCNA_', save=True)

print( pyWGCNA_m1_10x.geneExpr.to_df().head(5) )

pyWGCNA_m1_10x.preprocess()

pyWGCNA_m1_10x.findModules()

pyWGCNA_m1_10x.updateSampleInfo(path='/Users/manojkumarsingh/PyWGCNA_/sample_info.csv', sep=',')

pyWGCNA_m1_10x.setMetadataColor('Sex', {'F': 'green',
'M': 'yellow'})
pyWGCNA_m1_10x.setMetadataColor('Genotype', {'Nothing': 'darkviolet',
'Something': 'deeppink'})
pyWGCNA_m1_10x.setMetadataColor('Age', {'0': 'thistle',
'1': 'purple'})
pyWGCNA_m1_10x.setMetadataColor('Tissue', {'M1': 'red',
'Cortex': 'blue'})

geneList = PyWGCNA.getGeneList(dataset='hsapiens_gene_ensembl', attributes=['ensembl_gene_id', 'external_gene_name', 'gene_biotype'], maps=['gene_id', 'gene_name', 'gene_biotype'])

pyWGCNA_m1_10x.updateGeneInfo(geneList)

pyWGCNA_m1_10x.analyseWGCNA()

pyWGCNA_m1_10x.saveWGCNA()

import PyWGCNA

pyWGCNA_m1_10x = PyWGCNA.readWGCNA("m1_10x.p")

print(pyWGCNA_m1_10x.datExpr.var.head(5) )

pyWGCNA_m1_10x.CoexpressionModulePlot(modules=["silver"], numGenes=10, numConnections=100, minTOM=0)
modules = pyWGCNA_m1_10x.datExpr.var.moduleColors.unique().tolist()
print( modules )
pyWGCNA_m1_10x.CoexpressionModulePlot(modules=modules, numGenes=10, numConnections=100, minTOM=0, file_name="all")

from pywgcna.

Hi,

I was able to run your code without any problem and gave me what it suppose to give! The only thing I changed is the outputPath which I don't believe is related to the error you got!

I would check the version of packages you have. I have listed mine here

for example this is what I got for silver module

from pywgcna.