From 2e7f6306007dafa428f83e2fd87250c0690b114f Mon Sep 17 00:00:00 2001
From: Tejas Kumar <157981948+patturtejaskumar@users.noreply.github.com>
Date: Tue, 18 Mar 2025 23:36:18 +0100
Subject: [PATCH] Create bidcell.py

---
 bidcell.py | 125 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 125 insertions(+)
 create mode 100644 bidcell.py

diff --git a/bidcell.py b/bidcell.py
new file mode 100644
index 00000000..09caf180
--- /dev/null
+++ b/bidcell.py
@@ -0,0 +1,125 @@
+import spatialdata as sd
+import spatialdata_plot as pl
+import matplotlib.pyplot as plt
+import numpy as np
+import tifffile
+import cv2
+import dask.dataframe as dd  #dask.dataframe should only be imported after spatial data to avoid prevent dependency conflicts
+import scanpy as sc
+import pandas as pd
+import natsort
+import os 
+from bidcell import BIDCellModel
+
+
+# preprocessing test data to get required input files for BIDcell
+sdata = sd.read_zarr("dataset.zarr")
+sdata_genes = sdata['transcripts']["feature_name"].unique().compute().sort_values().tolist()
+# Extracting DAPI image from dataset.zarr
+image_pyramid = []
+img = sdata["morphology_mip"]["/scale0"]["image"].values  # Convert dask array to numpy
+img = np.squeeze(img)  # Remove singleton channel dimension (c:1)
+image_pyramid.append(img)
+
+with tifffile.TiffWriter( "morphology_mip_pyramidal.tiff", bigtiff=True) as tiff:
+    for img in image_pyramid:
+        tiff.write(img, photometric="minisblack", resolution=(1, 1))
+
+
+#Converting h5ad single cell reference to .csv
+adata = sc.read_h5ad("dataset.h5ad")
+shared_genes = [g for g in sdata_genes if g in adata.var["feature_name"].values] #crucial to avoid key error due to discrepencies in the genes present
+adata = adata[:, adata.var["feature_name"].isin(shared_genes)]
+
+# Set var_names to feature_name
+adata.var_names = adata.var["feature_name"].astype(str)
+sc_ref = pd.DataFrame(
+    data=adata[:, shared_genes].layers["normalized"].toarray(), 
+    columns=shared_genes, 
+    index=range(adata.n_obs)
+)
+celltypes = adata.obs['cell_type'].unique().tolist()
+cell_type_col = adata.obs['cell_type'].astype('category')
+sc_ref["ct_idx"] = cell_type_col.cat.codes.values
+sc_ref["cell_type"] = cell_type_col.values
+sc_ref["atlas"] = "custom"
+sc_ref.to_csv( "scref.csv")
+
+# generating transcript map .csv from test data
+transcript = sdata["transcripts"].compute()
+transcript=pd.DataFrame(transcript)
+#transcript.to_csv(filename="transcript.csv.gz", single_file=True, compression='gzip') #to generate transcript file without the filter
+transcript[transcript["feature_name"].isin(shared_genes)].to_csv("transcript.csv.gz",compression='gzip'
+)
+
+
+#generating positive and negative marker files from the single cell reference
+# defining the function generate_markers
+
+def generate_markers(ref_df, max_overlaps_pos=4, max_overlaps_neg=15):
+    """
+    Generate positive and negative marker dataframes from reference data.
+    
+    Args:
+        ref_df (pd.DataFrame): Reference dataframe with gene expression data and cell type info
+        max_overlaps_pos (int): Maximum number of cell types that can share a positive marker
+        max_overlaps_neg (int): Maximum number of cell types that can share a negative marker
+    
+    Returns:
+        tuple: (df_pos, df_neg) - DataFrames containing positive and negative markers
+    """
+
+    n_genes = ref_df.shape[1] - 3
+    cell_types = natsort.natsorted(list(set(ref_df["cell_type"].tolist())))
+    n_cell_types = len(cell_types)
+    
+    ref_expr = ref_df.iloc[:, :n_genes].to_numpy()
+    gene_names = ref_df.columns[:n_genes]
+    ct_idx = ref_df["ct_idx"].to_numpy()
+
+    # Generate negative markers
+    pct_10 = np.percentile(ref_expr, 10, axis=1, keepdims=True)
+    pct_10 = np.tile(pct_10, (1, n_genes))
+    low_expr_true = np.zeros(pct_10.shape)
+    low_expr_true[ref_expr <= pct_10] = 1
+
+    low_expr_true_agg = np.zeros((n_cell_types, n_genes))
+    for ct in range(n_cell_types):
+        rows = np.where(ct_idx == ct)[0]
+        low_expr_true_ct = low_expr_true[rows]
+        low_expr_true_agg[ct, :] = np.prod(low_expr_true_ct, axis=0)
+
+    overlaps = np.sum(low_expr_true_agg, 0)
+    too_many = np.where(overlaps > max_overlaps_neg)[0]
+    low_expr_true_agg[:, too_many] = 0
+    df_neg = pd.DataFrame(low_expr_true_agg, index=cell_types, columns=gene_names)
+
+    # Generate positive markers
+    pct_90 = np.percentile(ref_expr, 90, axis=1, keepdims=True)
+    pct_90 = np.tile(pct_90, (1, n_genes))
+    high_expr_true = np.zeros(pct_90.shape)
+    high_expr_true[ref_expr >= pct_90] = 1
+
+    high_expr_true_agg = np.zeros((n_cell_types, n_genes))
+    for ct in range(n_cell_types):
+        rows = np.where(ct_idx == ct)[0]
+        high_expr_true_ct = high_expr_true[rows]
+        high_expr_true_agg[ct, :] = np.prod(high_expr_true_ct, axis=0)
+
+    overlaps = np.sum(high_expr_true_agg, 0)
+    too_many = np.where(overlaps > max_overlaps_pos)[0]
+    high_expr_true_agg[:, too_many] = 0
+    df_pos = pd.DataFrame(high_expr_true_agg, index=cell_types, columns=gene_names)
+
+    return df_pos, df_neg
+
+# generate positive and negative marker files 
+df_pos, df_neg = generate_markers(sc_ref, max_overlaps_pos=4, max_overlaps_neg=15)
+df_pos.to_csv( "pos_marker.csv")
+df_neg.to_csv("neg_marker.csv")
+
+
+# Setting up and running BIDCell
+model = BIDCellModel("testdata.yaml")
+model.run_pipeline() 
+