API

Import scButterfly:

import scButterfly

butterfly

butterfly.Butterfly()
butterfly.Butterfly.load_data(RNA_data, ...)	Load data to Butterfly model.
butterfly.Butterfly.data_preprocessing([...])	Preprocessing for RNA data and ATAC data in Butterfly.
butterfly.Butterfly.augmentation([aug_type, ...])	Data augmentation for Butterfly model.
butterfly.Butterfly.construct_model(chrom_list)	Main model.
butterfly.Butterfly.train_model([...])	Training for model.
butterfly.Butterfly.test_model([batch_size, ...])	Test for model.

calculate_cluster

calculate_cluster.calculate_cluster_index(adata)

Evaluation of cluster index of prediction.

data_processing

data_processing.inverse_TFIDF(TDIDFed_mat, ...)	Inversed TF-IDF transformation for matrix.
data_processing.RNA_data_preprocessing(RNA_data)	Preprocessing for RNA data, we choose normalization, log transformation and highly variable genes, using scanpy.
data_processing.ATAC_data_preprocessing(...)	Preprocessing for ATAC data, we choose binarize, peaks filtering, TF-IDF transformation and scale transformation, using scanpy.
data_processing.CLR_transform(ADT_data)	Centered log-ratio transformation for ADT data.

draw_cluster

draw_cluster.draw_tsne(data, title, color)

Visualization of prediction using tSNE Algorithm.

train_model

train_model.Model(RNA_data, ATAC_data, ...)
train_model.Model.train(loss_weight, ...[, ...])	Training for model.
train_model.Model.test(test_id_r, test_id_a, ...)	Test for model.

train_model_cite

train_model_cite.Model(RNA_data, ATAC_data, ...)
train_model_cite.Model.train(loss_weight, ...)	Training for model.
train_model_cite.Model.test(test_id_r, test_id_a)	Test for model.

train_model_perturb

train_model_perturb.Model(RNA_data, ...[, ...])
train_model_perturb.Model.train(loss_weight, ...)	Training for model.
train_model_perturb.Model.test(test_id_r, ...)	Test for model.