Source code for stlearn.adds.parsing

from typing import Optional, Union
from anndata import AnnData
from matplotlib import pyplot as plt
from pathlib import Path
import os
import sys
import numpy as np

[docs]def parsing( adata: AnnData, coordinates_file: Union[Path, str], copy: bool = True, ) -> Optional[AnnData]: """\ Parsing the old spaital transcriptomics data Parameters ---------- adata Annotated data matrix. coordinates_file Coordinate file generated by st_spot_detector. copy Return a copy instead of writing to adata. Returns ------- Depending on `copy`, returns or updates `adata` with the following fields. **imagecol** and **imagerow** : `adata.obs` field Spatial information of the tissue image. """ # Get a map of the new coordinates new_coordinates = dict() with open(coordinates_file, "r") as filehandler: for line in filehandler.readlines(): tokens = line.split() assert len(tokens) >= 6 or len(tokens) == 4 if tokens[0] != "x": old_x = int(tokens[0]) old_y = int(tokens[1]) new_x = round(float(tokens[2]), 2) new_y = round(float(tokens[3]), 2) if len(tokens) >= 6: pixel_x = float(tokens[4]) pixel_y = float(tokens[5]) new_coordinates[(old_x, old_y)] = (pixel_x, pixel_y) else: raise ValueError( "Error, output format is pixel coordinates but\n " "the coordinates file only contains 4 columns\n" ) counts_table = adata.to_df() new_index_values = list() imgcol = [] imgrow = [] for index in counts_table.index: tokens = index.split("x") x = int(tokens[0]) y = int(tokens[1]) try: new_x, new_y = new_coordinates[(x, y)] imgcol.append(new_x) imgrow.append(new_y) new_index_values.append("{0}x{1}".format(new_x, new_y)) except KeyError: counts_table.drop(index, inplace=True) # Assign the new indexes # counts_table.index = new_index_values # Remove genes that have now a total count of zero counts_table = counts_table.transpose()[counts_table.sum(axis=0) > 0].transpose() adata = AnnData(counts_table) adata.obs["imagecol"] = imgcol adata.obs["imagerow"] = imgrow adata.obsm["spatial"] = np.c_[[imgcol, imgrow]].reshape(-1, 2) return adata if copy else None