Atlas construction

Generating training data for MIDAS

Rscript preprocess/combine_subsets.R --task atlas && py preprocess/split_mat.py --task atlas &

Training MIDAS

CUDA_VISIBLE_DEVICES=0 py run.py --exp e0 --task atlas

Inferring latent variables, and generating imputed and batch corrected counts

CUDA_VISIBLE_DEVICES=0 py run.py --task atlas --act predict_all_latent_bc --init_model sp_latest &

Evaluation

UMAP visualization of the joint embeddings generated by MIDAS in atlas construction:

Rscript comparison/vis_z_atlas.r --init_model sp_latest --task atlas