header=None)
pd.Series(dataset.barcode).to_csv(imputed_dir + 'barcode.txt',
sep='\t',
index=False,
header=None)
elif args.impute:
print("Saving imputed data")
recon_x = pd.DataFrame(recon_x.T,
index=dataset.peaks,
columns=dataset.barcode)
recon_x.to_csv(os.path.join(outdir, 'imputed_data.txt'), sep='\t')
# torch.save(model.to('cpu').state_dict(), os.path.join(outdir, 'model.pt')) # save model
# if not args.no_tsne:
print("Plotting embedding")
if args.reference:
ref = pd.read_csv(args.reference, sep='\t', header=None,
index_col=0)[1]
labels = ref.reindex(dataset.barcode, fill_value='unknown')
else:
labels = pred
plot_embedding(feature,
labels,
method=args.emb,
save=os.path.join(outdir, 'emb_{}.pdf'.format(args.emb)),
save_emb=os.path.join(outdir,
'emb_{}.txt'.format(args.emb)))
# plot_embedding(feature, labels,
# save=os.path.join(outdir, 'tsne.pdf'), save_emb=os.path.join(outdir, 'tsne.txt'))
# 3. imputed data
if args.impute or args.binary:
recon_x = model.encodeBatch(testloader, device, out='x', transforms=[normalizer.inverse_transform])
if args.binary:
import scipy
print("Saving binary imputed data")
recon_x = binarization(recon_x, dataset.data).T
imputed_dir = outdir+'/binary_imputed/'
os.makedirs(imputed_dir, exist_ok=True)
scipy.io.mmwrite(imputed_dir+'count.mtx', recon_x)
pd.Series(dataset.peaks).to_csv(imputed_dir+'peak.txt', sep='\t', index=False, header=None)
pd.Series(dataset.barcode).to_csv(imputed_dir+'barcode.txt', sep='\t', index=False, header=None)
elif args.impute:
print("Saving imputed data")
recon_x = pd.DataFrame(recon_x.T, index=dataset.peaks, columns=dataset.barcode)
recon_x.to_csv(os.path.join(outdir, 'imputed_data.txt'), sep='\t')
# torch.save(model.to('cpu').state_dict(), os.path.join(outdir, 'model.pt')) # save model
if not args.no_tsne:
print("Plotting tSNE embedding")
if args.reference:
ref = pd.read_csv(args.reference, sep='\t', header=None, index_col=0)[1]
labels = ref.reindex(dataset.barcode, fill_value='unknown')
else:
labels = pred
plot_embedding(feature, labels,
save=os.path.join(outdir, 'tsne.pdf'), save_emb=os.path.join(outdir, 'tsne.txt'))