Move more code over to the plugin from core

Author: ewels

multiqc_xenium_extra/xenium_extra.py

@@ -2,7 +2,7 @@
 
 import logging
 from pathlib import Path
-from typing import Any, Dict, Optional
+from typing import Any, Dict, Optional, Tuple
 
 import importlib_metadata
 import numpy as np
@@ -14,11 +14,43 @@
 from multiqc.plots import bargraph, box, linegraph, scatter, table
 from multiqc.plots.table_object import ColumnDict, TableConfig
 from multiqc.utils import mqc_colour
-from multiqc.modules.xenium.xenium import GENE_CATS, categorize_feature
 
 log = logging.getLogger("multiqc")
 
 
+# Define gene categories for coloring based on Xenium naming conventions
+GENE_CATS = {
+    "Pre-designed": {"color": "rgba(31, 119, 180, 0.8)"},  # Standard gene names - blue with transparency
+    "Custom": {"color": "rgba(255, 127, 14, 0.8)"},  # Orange with transparency
+    "Negative Control Probe": {"color": "rgba(214, 39, 40, 0.8)"},  # Red with transparency
+    "Negative Control Codeword": {"color": "rgba(255, 153, 0, 0.8)"},  # Yellow/Orange with transparency
+    "Genomic Control Probe": {"color": "rgba(227, 119, 194, 0.8)"},  # Pink with transparency
+    "Unassigned Codeword": {"color": "rgba(127, 127, 127, 0.8)"},  # Gray with transparency
+    "Deprecated Codeword": {"color": "rgba(188, 189, 34, 0.8)"},  # Olive with transparency
+}
+
+
+def categorize_feature(feature_name) -> Tuple[str, str]:
+    """Categorize a feature based on its name
+    Splits the feature name into category and feature id"""
+    # Check prefixes directly instead of using regex for better performance
+    category = ""
+    feature_id = feature_name.split("_")[1] if "_" in feature_name else feature_name
+    if feature_name.startswith("Custom_"):
+        category = "Custom"
+    elif feature_name.startswith("NegControlProbe_"):
+        category = "Negative Control Probe"
+    elif feature_name.startswith("NegControlCodeword_"):
+        category = "Negative Control Codeword"
+    elif feature_name.startswith("GenomicControlProbe_"):
+        category = "Genomic Control Probe"
+    elif feature_name.startswith("UnassignedCodeword_"):
+        category = "Unassigned Codeword"
+    else:
+        category = "Pre-designed"  # Default category for standard gene names
+    return category, feature_id
+
+
 def xenium_extra_execution_start():
     """Code to execute after config files and command line flags have been parsed.
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "multiqc_xenium_extra"
-version = "1.0.0"
+version = "1.0.1"
 authors = [
     {name = "Phil Ewels", email = "phil.ewels@seqera.io"},
 ]