Quickstart

import re
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
import alphashape
import scanpy as sc
import pandas as pd

import sys
sys.path.append('/Users/koush/Projects/SpaceOracle/src')

# Human Tonsil snRNAseq from SlideTags
# https://www.nature.com/articles/s41586-023-06837-4

adata = sc.read_h5ad('/Users/koush/Projects/SpaceOracle/data/snrna_germinal_center.h5ad')
adata

AnnData object with n_obs × n_vars = 1309 × 3333
    obs: 'cell_type', 'cell_type_2', 'cell_type_int', 'colors', 'cell_type_major'
    obsm: 'X_umap', 'spatial'
    layers: 'raw_count'

from SpaceTravLR.spaceship import SpaceShip

# Note: Make sure the outdir matches the one in the launch.py file

spacetravlr = SpaceShip(
    name='myTonsil', 
    outdir='/tmp/output'
)

spacetravlr.setup_(adata, overwrite=True, run_commot=False)

                                       ✅ NicheNet: Complete                                        

Imputing clusterwise 100%|██████████████████████████████████████| 3/3 [00:11<00:00, 0.26 clusters/s]

OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.

<SpaceTravLR.spaceship.SpaceShip at 0x3572ee640>

assert spacetravlr.is_everything_ok()

We're going on a trip in our favorite rocket ship 🚀️

## Run this multiple times to spawn parallel workers
spacetravlr.spawn_worker(
    partition='GPU-shared',
    clusters='bridges2',
    gres='gpu:1',
    job_name='SpaceTravLR',
    lifespan=1,
    python_path='/jet/home/awang22/.conda/envs/sheep/bin/python'
) 

Submitted batch job 35933180 on cluster bridges2

spacetravlr.setup_perturbations(
    adata=adata, 
    use_float16=True
)

                               FOXO1 -> 0 - 4/4 - Completed in 18.68s                               

Reading betadata files 100%|██████████████████████████████████| 10/10 [00:00<00:00, 49.11 parquet/s]

spacetravlr.perturb(
    target='FOXO1',
    propagation=4,
    gene_expr=0,
)