spateo.external.CAST.main

Functions

CAST_MARK(coords_raw_t, exp_dict_t, output_path_t[, ...])

CAST_STACK(coords_raw, embed_dict, output_path, graph_list)

CAST_PROJECT(sdata_inte, source_sample, target_sample, ...)

Module Contents

spateo.external.CAST.main.CAST_MARK(coords_raw_t, exp_dict_t, output_path_t, task_name_t=None, gpu_t=None, args=None, epoch_t=None, if_plot=True, graph_strategy='convex', device='cuda:0')[source]
spateo.external.CAST.main.CAST_STACK(coords_raw, embed_dict, output_path, graph_list, params_dist=None, tmp1_f1_idx=None, mid_visual=False, sub_node_idxs=None, rescale=False, corr_q_r=None, if_embed_sub=False, early_stop_thres=None, renew_mesh_trans=True)[source]
spateo.external.CAST.main.CAST_PROJECT(sdata_inte, source_sample, target_sample, coords_source, coords_target, scaled_layer='log2_norm1e4_scaled', raw_layer='raw', batch_key='protocol', use_highly_variable_t=True, ifplot=True, n_components=50, umap_n_neighbors=50, umap_n_pcs=30, min_dist=0.01, spread_t=5, k2=1, source_sample_ctype_col='level_2', output_path='', umap_feature='X_umap', pc_feature='X_pca_harmony', integration_strategy='Harmony', ave_dist_fold=3, save_result=True, ifcombat=True, alignment_shift_adjustment=50, color_dict=None, adjust_shift=False, metric_t='cosine', working_memory_t=1000)[source]