| """Layer name constants and defaults for scPTR.""" | |
| # Layer names | |
| UNSPLICED = "unspliced" | |
| SPLICED = "spliced" | |
| SMOOTHED_UNSPLICED = "Mu" | |
| SMOOTHED_SPLICED = "Ms" | |
| GAMMA = "gamma" | |
| PT_VELOCITY = "pt_velocity" | |
| VELOCITY_S = "velocity_S" | |
| # var columns | |
| BETA = "beta" | |
| TF_SCORE = "tf_score" | |
| PTF_SCORE = "ptf_score" | |
| # obs columns | |
| PT_STATE = "pt_state" | |
| # uns keys | |
| UNS_KEY = "scptr" | |
| # Defaults | |
| DEFAULT_N_NEIGHBORS = 30 | |
| DEFAULT_BANDWIDTH = "adaptive" | |
| DEFAULT_BETA_QUANTILE = 0.95 | |
| DEFAULT_CLIP_QUANTILE = 0.99 | |
| DEFAULT_GENE_BATCH_SIZE = 500 | |
| DEFAULT_LEIDEN_RESOLUTION = 1.0 | |
| DEFAULT_MIN_UNSPLICED_COUNTS = 10 | |
| DEFAULT_MIN_UNSPLICED_CELLS = 10 | |