cytocraft 0.0.9

The Cytocraft package provides prediction of chromosome conformation based on spatial transcriptomic.

Cytocraft

Overview

The Cytocraft package generates a 3D reconstruction of transcription centers with subcellular resolution spatial transcriptomics.

Installaion

pip install cytocraft

Interactive Mode Usage

import

from cytocraft.craft import *

read input

gem_path = './data/mice/example_scgem.csv'
gem = read_gem_as_csv(gem_path, sep=',')
adata = read_gem_as_adata(gem_path, sep=',', SN='example')
GeneUIDs = get_GeneUID(gem)

run cytocraft

adata = craft(
	gem=gem,
        adata=adata,
        species='Mice',
        seed=999,
        )

CLI Mode Usage

python craft.py [-h] [-p PERCENT] [-c CELLTYPE] [--ctkey CTKEY] [--cikey CIKEY] [--seed SEED] gem_path out_path {Human,Mouse,Axolotls,Monkey}

Positional arguments:

gem_path Input: path to gene expression matrix file

out_path Output: dir path to save results

{Human,Mouse,Axolotls,Monkey} Species of the input data

Optional arguments:

-h, --help show this help message and exit

-p, --percent percent of gene for rotation derivation, default: 0.001

-t, --threshold The maximum proportion of np.nans allowed in a column(gene) in W, default: 0.90

-c, --celltype Path of file containing cell types, multi-celltype mode only

--ctkey Key of celltype column in the cell type file, multi-celltype mode only

--cikey Key of cell id column in the cell type file, multi-celltype mode only

--seed Random seed, default: random int between 0 to 1000

One-celltype example:

python craft.py ./data/SS200000108BR_A3A4_scgem.Spinal_cord_neuron.csv ./results/ Mouse

Multi-celltype example:

python craft.py ./data/SSSS200000108BR_A3A4_scgem.csv ./results/ Mouse --celltype ./data/cell_feature.csv --ctkey cell_type --cikey cell_id