cytocraft 0.1.5

The Cytocraft package provides prediction of chromosome configuration based on subcellular resolution spatial transcriptomics.

Cytocraft

Overview

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

Installaion

pip install cytocraft

Interactive Mode Usage

import

import cytocraft.craft as cc

read input

gem_path = './data/mice/example_scgem.csv'
gem = cc.read_gem_as_csv(gem_path, sep=',')
adata = cc.read_gem_as_adata(gem_path, sep=',')

run cytocraft (quick start, see tutorial for more details)

adata = cc.craft(
  gem=gem,
  adata=adata,
  species='Mice',
  seed=999,
  samplename='example'
  )

CLI Mode Usage

python craft.py [-h] [-p/-n PERCENT/NUMBER] [-t GENE_FILTER_THRESH] [-r RMSD_THRESH] [--sep \t] [-c CELLTYPE] [--ctkey CTKEY] [--cikey CIKEY] [--csep \t] [--seed SEED] -i gem_path -o out_path --species {Human,Mouse,Axolotls,Monkey}

Positional arguments:

-i,--gem_path Input: Path of input gene expression matrix file

-o,--out_path Output: Directory to save results

--species Species of the input data, e.g. {Human,Mouse,Axolotls,Monkey}

Optional arguments:

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

-p/-n, --percent/--number Percent/Number of anchor gene for rotation derivation, default: 0.001/10

-t, --gene_filter_thresh The maximum allowable proportion of np.nan values in a column (representing a gene) of the observed transcription centers (Z), default: 0.90

-r, --rmsd_thresh RMSD threshold. If the computed RMSD value is less than or equal to this threshold, it means the process has reached an acceptable level of similarity or convergence, and the loop is exited. default: 0.01

--sep Separator of the input gene expression matrix file

-c, --celltype Path of the annotation 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

--csep Separator of the annotation file, multi-celltype mode only, default: \t

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

One-celltype example:

python craft.py -i ./data/SS200000108BR_A3A4_scgem.Spinal_cord_neuron.csv -o ./results/ --species Mouse

Multi-celltype example:

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