feat: adding custom arrow plot

README.md

@@ -121,6 +121,50 @@ Then genome-wide association signals are added as black dots. The size of the do
 
 Finally the `.png` file is saved (and `.svg` file if required).
 
+### Step 3 - Generate gene arrow plot
+
+The `plot-gene-arrow` command generates a gene structure diagram (arrow plot) for a specific gene, showing its exons, UTRs, and strand direction.
+
+```bash
+uv run plot-gene-arrow --gene TSPAN6 --data-folder data_folder/ --config config.json
+```
+
+help output:
+
+```text
+usage: plot_gene_arrow.py [-h] -g GENE -d DATA_FOLDER -c CONFIG [-o OUTPUT] [-w ARROW_WIDTH]
+
+Generate an arrow plot (gene structure diagram) for a given gene.
+See github: https://github.com/DSuveges/GenomePlotter
+
+options:
+  -h, --help            show this help message and exit
+  -g GENE, --gene GENE  Gene name (e.g. BRCA1)
+  -d DATA_FOLDER, --data-folder DATA_FOLDER
+                        Path to the data folder containing processed files
+  -c CONFIG, --config CONFIG
+                        Path to config JSON file
+  -o OUTPUT, --output OUTPUT
+                        Output file basename (defaults to {gene_name}_arrow)
+  -w ARROW_WIDTH, --arrow-width ARROW_WIDTH
+                        Arrow height in pixels (default: 10)
+```
+
+The script reads the pre-processed GENCODE arrow file from the data folder (generated in Step 1), filters it for the requested gene, and renders the gene structure as an SVG and PNG. Both files are saved using the output basename.
+
+**Examples:**
+
+```bash
+# Generate arrow plot for TSPAN6 using default output name (TSPAN6_arrow.svg / TSPAN6_arrow.png):
+uv run plot-gene-arrow -g TSPAN6 -d data_folder/ -c config.json
+
+# Specify a custom output basename:
+uv run plot-gene-arrow -g BRCA1 -d data_folder/ -c config.json -o plots/BRCA1_structure
+
+# Adjust arrow height:
+uv run plot-gene-arrow -g TP53 -d data_folder/ -c config.json -w 15
+```
+
 ### Gene sets
 
 The `gene_sets/` folder contains a set of files that can be used as gene annotation:

pyproject.toml

@@ -14,6 +14,7 @@ dependencies = [
     "requests>=2.32.4",
     "pyyaml>=6.0.2",
     "cairosvg>=2.7.1",
+    "loguru>=0.7.0",
 ]
 
 [project.optional-dependencies]
@@ -29,6 +30,7 @@ dev = [
 [project.scripts]
 prepare-data = "genome_plotter.prepare_data:main"
 plot-chromosome = "genome_plotter.plot_chromosome:main"
+plot-gene-arrow = "genome_plotter.plot_gene_arrow:main"
 
 [build-system]
 requires = ["hatchling"]

src/genome_plotter/__init__.py

@@ -3,3 +3,5 @@
 from __future__ import annotations
 
 __version__ = "0.1.0"
+
+LOG_FORMAT = "{time:YYYY-MM-DD HH:mm:ss} {level} {module} - {function}: {message}"

src/genome_plotter/assets/config.json

@@ -25,8 +25,8 @@
     "gwas_point": "#000000",
     "arrow_colors": {
       "line_color": "#6495ED",
-      "utr_color": "#FFE4B5",
-      "cds_color": "#ADD8E6"
+      "utr_color": "#CE93D8",
+      "cds_color": "#F4A460"
     },
     "cytoband_colors": {
       "gneg": "#FFFFFF",

src/genome_plotter/functions/ChromosomePlotter.py

@@ -2,15 +2,13 @@
 
 from __future__ import annotations
 
-import logging
 import os
 
 os.environ["DYLD_FALLBACK_LIBRARY_PATH"] = "/opt/homebrew/lib"
 
 import cairosvg
 import pandas as pd
-
-logger = logging.getLogger(__name__)
+from loguru import logger
 
 
 class ChromosomePlotter:

src/genome_plotter/functions/ColorFunctions.py

@@ -3,11 +3,11 @@
 from __future__ import annotations
 
 import colorsys
-import logging
 import re
 
 import numpy as np
 import pandas as pd
+from loguru import logger
 
 
 def hex_to_rgb(hex_color: str) -> list[int]:
@@ -199,17 +199,20 @@ def __init__(
                     'All colors should be in hexadecimal format eg "#1ED5FA"'
                 )
 
-        # Checking dark max and the threshold:
-        for val in [dark_max, dark_threshold]:
-            if (not isinstance(val, float)) or (val >= 1) or (val <= 0):
+        # Validate darkening parameters only when they are provided:
+        if dark_max is not None or dark_threshold is not None:
+            for val in [dark_max, dark_threshold]:
+                if not isinstance(val, float) or (val >= 1) or (val <= 0):
+                    raise ValueError(
+                        f"dark_max and dark_threshold has to be float between 0 and 1 instead: {val}"
+                    )
+            if not isinstance(width, int):
                 raise ValueError(
-                    f"dark_max and dark_threshold has to be float between 0 and 1 instead: {val}"
+                    f"width must be an integer when darkening is enabled. Got: {width}"
                 )
 
-        # Checking dark max and the threshold:
-        for val in [count, width]:
-            if not isinstance(val, int):
-                raise ValueError(f"Count and width have to be integers. Got: {val}")
+        if not isinstance(count, int):
+            raise ValueError(f"count has to be an integer. Got: {count}")
 
         # Generating color gradients for a given length:
         self.color_map = {
@@ -239,7 +242,7 @@ def map_color(self: ColorPicker, feature: str, gc_content: float | None) -> str:
             try:
                 color = self.color_map[feature][int(gc_content * (self.count - 1))]
             except KeyError:
-                logging.error(
+                logger.error(
                     f"Feature {feature} was not found in color mapper. Returning black."
                 )
                 color = "#000000"