net_post.findModules(
kwargs_function={
'cutreeHybrid': {
'deepSplit': 3,
'pamRespectsDendro': True,
},
"pickSoftThreshold": {
"blockSize": 5000
},
}
)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[38], line 3
1 net_post.MEDissThres = 0.01
----> 3 net_post.findModules(
4 kwargs_function={
5 'cutreeHybrid': {
6 'deepSplit': 3,
7 'pamRespectsDendro': True,
8 # "cutHeight": 0.998,
9 # "pamStage": False,
10 },
11 "pickSoftThreshold": {
12 "blockSize": 5000
13 },
14 },
15 # skip_steps=["pickSoftThreshold", "adjacency", "TOMsimilarity", "linkage", "cutreeHybrid"],
16 force_power=7
17 )
File ~/.conda/envs/rnaseq/lib/python3.13/site-packages/PyWGCNA/wgcna.py:367, in WGCNA.findModules(self, kwargs_function, skip_steps, force_power)
364 dissTOM = 1 - self.TOM
365 dissTOM = dissTOM.round(decimals=8)
--> 367 dynamicMods = WGCNA.cutreeHybrid(dendro=self.geneTree, distM=dissTOM, minClusterSize=self.minModuleSize,
368 **kwargs)
371 # Convert numeric labels into colors
372 kwargs = dict()
File ~/.conda/envs/rnaseq/lib/python3.13/site-packages/PyWGCNA/wgcna.py:1821, in WGCNA.cutreeHybrid(dendro, distM, cutHeight, minClusterSize, deepSplit, maxCoreScatter, minGap, maxAbsCoreScatter, minAbsGap, minSplitHeight, minAbsSplitHeight, externalBranchSplitFnc, nExternalSplits, minExternalSplit, externalSplitOptions, externalSplitFncNeedsDistance, assumeSimpleExternalSpecification, pamStage, pamRespectsDendro, useMedoids, maxPamDist, respectSmallClusters)
1819 basicOnBranch = branch_basicClusters[onBr[0] - 1]
1820 labelsOnBranch = branchLabels[basicOnBranch - 1]
-> 1821 useObjects = ColorsX in np.unique(labelsOnBranch)
1822 DistSClustClust = distM.iloc[InCluster, useObjects]
1823 MeanDist = DistSClustClust.mean(axis=0)
ValueError: operands could not be broadcast together with shapes (2,) (21902,)`
Running this code:
results in:
whereas running the same code with
pamRespectsDendro=Falseworks fine. What can be the problem?