def ldvae_benchmark(dataset, n_epochs, use_cuda=True):
ldvae = LDVAE(dataset.nb_genes, n_batch=dataset.n_batches)
trainer = UnsupervisedTrainer(ldvae, dataset, use_cuda=use_cuda)
trainer.train(n_epochs=n_epochs)
trainer.test_set.reconstruction_error()
trainer.test_set.marginal_ll()
ldvae.get_loadings()
return trainer
def scVI_ld(csv_file, csv_path, ndims, vae_model = VAE, n_labels = 0, n_cores=1, seed= 1234, lr = 1e-3, use_cuda = False):
set_seed(seed)
dat = CsvDataset(csv_file,
save_path=csv_path,
new_n_genes=None)
# Based on recommendations in linear_decoder.ipynb
n_epochs = 250
# trainer and model
ldvae = LDVAE(
dat.nb_genes,
n_batch = dat.n_batches,
n_latent = ndims,
n_labels = n_labels
)
trainerLD = UnsupervisedTrainer(ldvae, dat, use_cuda=use_cuda)
# limit cpu usage
torch.set_num_threads(n_cores)
trainerLD.train(n_epochs=n_epochs, lr=lr)
# extract mean value for the ld
full = trainerLD.create_posterior(trainerLD.model, dat, indices=np.arange(len(dat)))
Z_hat = full.sequential().get_latent()[0]
adata = anndata.AnnData(dat.X)
for i, z in enumerate(Z_hat.T):
adata.obs[f'Z_{i}'] = z
# reordering for convenience and correspondance with PCA's ordering
cellLoads = adata.obs.reindex(adata.obs.std().sort_values().index, axis = 1)
return(cellLoads)
def scvi(
adata: AnnData,
n_hidden: int = 128,
n_latent: int = 10,
n_layers: int = 1,
dispersion: str = "gene",
n_epochs: int = 400,
lr: int = 1e-3,
train_size: int = 1.0,
batch_key: Optional[str] = None,
use_highly_variable_genes: bool = True,
subset_genes: Optional[Sequence[Union[int, str]]] = None,
linear_decoder: bool = False,
copy: bool = False,
use_cuda: bool = True,
return_posterior: bool = True,
trainer_kwargs: dict = {},
model_kwargs: dict = {},
) -> Optional[AnnData]:
"""\
SCVI [Lopez18]_.
Fits scVI model onto raw count data given an anndata object
scVI uses stochastic optimization and deep neural networks to aggregate information
across similar cells and genes and to approximate the distributions that underlie
observed expression values, while accounting for batch effects and limited sensitivity.
To use a linear-decoded Variational AutoEncoder model (implementation of [Svensson20]_.),
set linear_decoded = True. Compared to standard VAE, this model is less powerful, but can
be used to inspect which genes contribute to variation in the dataset. It may also be used
for all scVI tasks, like differential expression, batch correction, imputation, etc.
However, batch correction may be less powerful as it assumes a linear model.
.. note::
More information and bug reports `here <https://github.com/YosefLab/scVI>`__.
Parameters
----------
adata
An anndata file with `X` attribute of unnormalized count data
n_hidden
Number of nodes per hidden layer
n_latent
Dimensionality of the latent space
n_layers
Number of hidden layers used for encoder and decoder NNs
dispersion
One of the following
* `'gene'` - dispersion parameter of NB is constant per gene across cells
* `'gene-batch'` - dispersion can differ between different batches
* `'gene-label'` - dispersion can differ between different labels
* `'gene-cell'` - dispersion can differ for every gene in every cell
n_epochs
Number of epochs to train
lr
Learning rate
train_size
The train size, either a float between 0 and 1 or an integer for the number of training samples to use
batch_key
Column name in anndata.obs for batches.
If None, no batch correction is performed
If not None, batch correction is performed per batch category
use_highly_variable_genes
If true, uses only the genes in anndata.var["highly_variable"]
subset_genes
Optional list of indices or gene names to subset anndata.
If not None, use_highly_variable_genes is ignored
linear_decoder
If true, uses LDVAE model, which is an implementation of [Svensson20]_.
copy
If true, a copy of anndata is returned
return_posterior
If true, posterior object is returned
use_cuda
If true, uses cuda
trainer_kwargs
Extra arguments for UnsupervisedTrainer
model_kwargs
Extra arguments for VAE or LDVAE model
Returns
-------
If `copy` is true, anndata is returned.
If `return_posterior` is true, the posterior object is returned
If both `copy` and `return_posterior` are true,
a tuple of anndata and the posterior are returned in that order.
`adata.obsm['X_scvi']` stores the latent representations
`adata.obsm['X_scvi_denoised']` stores the normalized mean of the negative binomial
`adata.obsm['X_scvi_sample_rate']` stores the mean of the negative binomial
If linear_decoder is true:
`adata.uns['ldvae_loadings']` stores the per-gene weights in the linear decoder as a
genes by n_latent matrix.
"""
warnings.warn(
"scvi via scanpy external API is no longer supported. " +
"Please use the new scvi-tools package from `scvi-tools.org`",
FutureWarning,
)
try:
from scvi.models import VAE, LDVAE
from scvi.inference import UnsupervisedTrainer
from scvi.dataset import AnnDatasetFromAnnData
except ImportError:
raise ImportError(
"Please install scvi package from https://github.com/YosefLab/scVI"
)
# check if observations are unnormalized using first 10
# code from: https://github.com/theislab/dca/blob/89eee4ed01dd969b3d46e0c815382806fbfc2526/dca/io.py#L63-L69
if len(adata) > 10:
X_subset = adata.X[:10]
else:
X_subset = adata.X
norm_error = (
'Make sure that the dataset (adata.X) contains unnormalized count data.'
)
if sp.sparse.issparse(X_subset):
assert (X_subset.astype(int) != X_subset).nnz == 0, norm_error
else:
assert np.all(X_subset.astype(int) == X_subset), norm_error
if subset_genes is not None:
adata_subset = adata[:, subset_genes]
elif use_highly_variable_genes and "highly_variable" in adata.var:
adata_subset = adata[:, adata.var["highly_variable"]]
else:
adata_subset = adata
if batch_key is not None:
codes, uniques = pd.factorize(adata_subset.obs[batch_key])
adata_subset.obs['_tmp_scvi_batch'] = codes
n_batches = len(uniques)
else:
n_batches = 0
dataset = AnnDatasetFromAnnData(adata_subset.copy(),
batch_label='_tmp_scvi_batch')
if linear_decoder:
vae = LDVAE(
n_input=dataset.nb_genes,
n_batch=n_batches,
n_labels=dataset.n_labels,
n_hidden=n_hidden,
n_latent=n_latent,
n_layers_encoder=n_layers,
dispersion=dispersion,
**model_kwargs,
)
else:
vae = VAE(
dataset.nb_genes,
n_batch=n_batches,
n_labels=dataset.n_labels,
n_hidden=n_hidden,
n_latent=n_latent,
n_layers=n_layers,
dispersion=dispersion,
**model_kwargs,
)
trainer = UnsupervisedTrainer(
model=vae,
gene_dataset=dataset,
use_cuda=use_cuda,
train_size=train_size,
**trainer_kwargs,
)
trainer.train(n_epochs=n_epochs, lr=lr)
full = trainer.create_posterior(trainer.model,
dataset,
indices=np.arange(len(dataset)))
latent, batch_indices, labels = full.sequential().get_latent()
if copy:
adata = adata.copy()
adata.obsm['X_scvi'] = latent
adata.obsm['X_scvi_denoised'] = full.sequential().get_sample_scale()
adata.obsm['X_scvi_sample_rate'] = full.sequential().imputation()
if linear_decoder:
loadings = vae.get_loadings()
df = pd.DataFrame(loadings, index=adata_subset.var_names)
adata.uns['ldvae_loadings'] = df
if copy and return_posterior:
return adata, full
elif copy:
return adata
elif return_posterior:
return full
