def test_scgen():
adata = scvi.data.synthetic_iid(run_setup_anndata=False)
setup_anndata(
adata,
batch_key="batch",
labels_key="labels",
)
model = SCGEN(adata)
model.train(
max_epochs=1, batch_size=32, early_stopping=True, early_stopping_patience=25
)
# batch Removal
model.batch_removal()
# predict
pred, delta = model.predict(
ctrl_key="batch_0", stim_key="batch_1", celltype_to_predict="label_0"
)
pred.obs["batch"] = "pred"
# reg mean and reg var
ctrl_adata = adata[
((adata.obs["labels"] == "label_0") & (adata.obs["batch"] == "batch_0"))
]
stim_adata = adata[
((adata.obs["labels"] == "label_0") & (adata.obs["batch"] == "batch_1"))
]
eval_adata = ctrl_adata.concatenate(stim_adata, pred, batch_key="concat_batches")
label_0 = adata[adata.obs["labels"] == "label_0"]
sc.tl.rank_genes_groups(label_0, groupby="batch", method="wilcoxon")
diff_genes = label_0.uns["rank_genes_groups"]["names"]["batch_1"]
model.reg_mean_plot(
eval_adata,
axis_keys={"x": "pred", "y": "batch_1"},
gene_list=diff_genes[:10],
labels={"x": "predicted", "y": "ground truth"},
save=False,
show=False,
legend=False,
)
base_path = '/Users/zhongyuanke/data/'
file_rna = '/Users/zhongyuanke/data/dann_vae/multimodal/rna.h5ad'
file_atac = '/Users/zhongyuanke/data/dann_vae/multimodal/atac.h5ad'
seurat_celltype_path = base_path + 'multimodal/atac_pbmc_10k/celltype_filt.csv'
batch_size = 128
adata1 = sc.read_h5ad(file_atac)
adata2 = sc.read_h5ad(file_rna)
print(adata1)
print(adata2)
# adata_b1.obs_names_make_unique()
# adata_b2.obs_names_make_unique()
# adata_b3.obs_names_make_unique()
adata_all = tl.davae_preprocessing([adata1, adata2], n_top_genes=2000, hvg=False, lognorm=False)
adata_all.obs_names_make_unique()
adata_all = scgen.setup_anndata(adata_all, batch_key="batch_label", copy=True)
model = scgen.SCGEN(adata_all)
model.train(max_epochs=15,
batch_size=32,
early_stopping=True,
early_stopping_patience=25,
use_gpu=False)
corrected_adata = model.batch_removal()
sc.pp.neighbors(corrected_adata,use_rep='corrected_latent')
sc.tl.umap(corrected_adata)
sc.pl.umap(corrected_adata,color='batch')
corrected_adata.write('/Users/zhongyuanke/data/scgen/scgen_multimodal.h5ad')