Trvae update to 1.1.2

[LuckyMD]

This PR updates the trVAE function to work with version 1.1.2

To do:

• update env
• test locally
• test on snakemake

[LuckyMD]

@M0hammadL please check if this looks correct to you!

[M0hammadL]

THIS line has to change to :
conditions = adata.obs[batch].unique().tolist() and then pass :

network = trvae.models.trVAE(x_dimension=adata.shape[1],
                                 architecture=[256,64],
                                 z_dimension=10,
                                 gene_names=adata.var_names.tolist(),
                                 conditions=conditions,
                                 model_path='/localscratch/',
                                 alpha=0.0001,
                                 beta=50,
                                 eta=100,
                                 loss_fn='sse',
                                 output_activation='linear')

[LuckyMD]

I see, so you have to pass a list of the batches rather than the name of the batch covariate. Thanks!

[LuckyMD]

THIS line has to change to :
conditions = adata.obs[batch].unique().tolist() and then pass :

network = trvae.models.trVAE(x_dimension=adata.shape[1],
                                 architecture=[256,64],
                                 z_dimension=10,
                                 gene_names=adata.var_names.tolist(),
                                 conditions=conditions,
                                 model_path='/localscratch/',
                                 alpha=0.0001,
                                 beta=50,
                                 eta=100,
                                 loss_fn='sse',
                                 output_activation='linear')

@M0hammadL addressed with commit c92622a . All good now?

[ilibarra]

@LuckyMD: What is the current status on running trVAE using scIB with snakemake? Would the latest trVAE version (1.1.2) work with the latest version of the scIB git? Maybe handled in another issue and overlooked it.

Thanks!

[LuckyMD]

trVAE from version 1.0 will only work with this PR, which we haven't merged yet, as it didn't pass initial testing.