AttributeError: Module 'scipy' has no attribute 'shape'

[nbutyrate]

Hi, I tgot following error after calling python from Reticulate, please help

mofa1 <- run_mofa(mofa)
Connecting to the mofapy2 python package using reticulate (use_basilisk = FALSE)...
Please make sure to manually specify the right python binary when loading R with reticulate::use_python(..., force=TRUE) or the right conda environment with reticulate::use_condaenv(..., force=TRUE)
If you prefer to let us automatically install a conda environment with 'mofapy2' installed using the 'basilisk' package, please use the argument 'use_basilisk = TRUE'

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use_float32 set to True: replacing float64 arrays by float32 arrays to speed up computations...

Successfully loaded view='Microbial_pathways' group='single_group' with N=16 samples and D=363 features...
Successfully loaded view='Microbial_Taxonomy' group='single_group' with N=16 samples and D=195 features...
Successfully loaded view='RNA' group='single_group' with N=16 samples and D=14324 features...

Warning: 6860 features(s) in view 2 have zero variance, consider removing them before training the model...

Model options:

• Automatic Relevance Determination prior on the factors: False
• Automatic Relevance Determination prior on the weights: True
• Spike-and-slab prior on the factors: False
• Spike-and-slab prior on the weights: False
  Likelihoods:
• View 0 (Microbial_pathways): gaussian
• View 1 (Microbial_Taxonomy): gaussian
• View 2 (RNA): gaussian

Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
AttributeError: Module 'scipy' has no attribute 'shape'
Run reticulate::py_last_error() for details.
In addition: Warning message:
In run_mofa(mofa) :
No output filename provided. Using /var/folders/3q/l3mk74214gb7n96bld12vg8h0000gn/T//RtmpQOMa72/mofa_20240326-142718.hdf5 to store the trained model.

[Rana-Sabrii]

Change s.shape to np.shape in the mofapy2/core/distributions/basic_distributions.py file and s.outer to np.outer in the mofapy2/core/BayesNet.py files.

[nbutyrate]

Thanks, it worked like magic, i have new error, please help

plot_weights_fn(mofa1, factor=1, view="Microbial_Taxonomy", nfeatures=8)
Error in plot_weights_fn(mofa1, factor = 1, view = "Microbial_Taxonomy", :
could not find function "plot_weights_fn"

packageVersion("MOFA2")
[1] ‘1.13.0’

[Rana-Sabrii]

can you give me the source where you get the code from?

[nbutyrate]

I am trying to follow this

https://raw.githack.com/bioFAM/MOFA2_tutorials/master/R_tutorials/microbiome_vignette.html

[Rana-Sabrii]

I tried to do so but i faced the same error😂 push it as a new issue may someone knows help

[artur-sannikov]

The links you published are outdated. I guess, the function plot_weights_fn is now called plot_weights. I opened #148. There you will find the link to the latest reference manual. For latest tutorials, see Bioconductor page.

[artur-sannikov]

I opened #157 for outdated links to tutorials.