diff --git a/README.md b/README.md
index e70ef91..8423a15 100644
--- a/README.md
+++ b/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:
diff --git a/pyproject.toml b/pyproject.toml
index de1e217..8b02226 100644
--- a/pyproject.toml
+++ b/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"]
diff --git a/src/genome_plotter/__init__.py b/src/genome_plotter/__init__.py
index 66e028c..6d96734 100644
--- a/src/genome_plotter/__init__.py
+++ b/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}"
diff --git a/src/genome_plotter/assets/config.json b/src/genome_plotter/assets/config.json
index c827402..3902a7f 100644
--- a/src/genome_plotter/assets/config.json
+++ b/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",
diff --git a/src/genome_plotter/functions/ChromosomePlotter.py b/src/genome_plotter/functions/ChromosomePlotter.py
index 3b7c390..9b7413f 100644
--- a/src/genome_plotter/functions/ChromosomePlotter.py
+++ b/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:
diff --git a/src/genome_plotter/functions/ColorFunctions.py b/src/genome_plotter/functions/ColorFunctions.py
index a63a861..ea7d8ba 100644
--- a/src/genome_plotter/functions/ColorFunctions.py
+++ b/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"
diff --git a/src/genome_plotter/functions/CustomGenePlotter.py b/src/genome_plotter/functions/CustomGenePlotter.py
index a0eba44..7fedc95 100644
--- a/src/genome_plotter/functions/CustomGenePlotter.py
+++ b/src/genome_plotter/functions/CustomGenePlotter.py
@@ -2,11 +2,12 @@
 
 from __future__ import annotations
 
-import logging
 from typing import TYPE_CHECKING
 
 import pandas as pd
+from loguru import logger
 
+from genome_plotter.functions.utils import Scaler
 from genome_plotter.input_parsers.data_integrator import DataIntegrator
 
 if TYPE_CHECKING:
@@ -29,7 +30,7 @@ def __init__(
         self.width = config_manager.plot_parameters.width
         self.gene_window = config_manager.plot_parameters.custom_gene_window
 
-        logging.info(f"Generating integrated dataset for gene: {query}")
+        logger.info(f"Generating integrated dataset for gene: {query}")
 
         # Reading gencode data:
         self.gencode_df = pd.read_csv(
@@ -51,10 +52,10 @@ def __init__(
         # Report what we have:
         self.gene_name = filtered_gencode.iloc[0]["gene_name"]
         self.gene_id = filtered_gencode.iloc[0]["gene_id"]
-        logging.info(
-            f"Gene name: {self.gene_name }, Ensembl gene identifier: {self.gene_id}"
+        logger.info(
+            f"Gene name: {self.gene_name}, Ensembl gene identifier: {self.gene_id}"
         )
-        logging.info(
+        logger.info(
             f"Number of gencode feature for this gene: {len(filtered_gencode):,}"
         )
 
@@ -64,19 +65,17 @@ def __init__(
         self.end = filtered_gencode.end.max()
         self.filtered_gencode = filtered_gencode
 
-        logging.info(f"Genomic coordinates: {self.chromosome}:{self.start}-{self.end}")
+        logger.info(f"Genomic coordinates: {self.chromosome}:{self.start}-{self.end}")
 
         # Get the relevant genome file:
         genome_file = config_manager.get_chromosome_file(self.chromosome)
         genome_df = self.__load_genome(genome_file)
-        logging.info(f"Number of genomic chunks for this gene: {len(genome_df)}")
+        logger.info(f"Number of genomic chunks for this gene: {len(genome_df)}")
 
         self.genome_df = genome_df
 
     @staticmethod
-    def __filter_gencode_data(
-        gene_name: str, gencode_df: pd.DataFrame
-    ) -> pd.DataFrame:
+    def __filter_gencode_data(gene_name: str, gencode_df: pd.DataFrame) -> pd.DataFrame:
         """Filter GENCODE data for a specific gene.
 
         Args:
@@ -180,17 +179,19 @@ class GenerateArrowPlot:
     ARROW_SVG = '<polygon points="{}" style="fill:{};stroke:{};stroke-width:1" />\n'
 
     def __init__(
-        self: GenerateArrowPlot, config_manager: Config, arrow_width: int
+        self: GenerateArrowPlot,
+        arrow_data: pd.DataFrame,
+        config_manager: Config,
+        scale_factor: int = 1,
     ) -> None:
         """Initialize the arrow plot generator.
 
         Args:
+            arrow_data (pd.DataFrame): dataframe with the arrow coordinates.
             config_manager (Config): Configuration manager object.
-            arrow_width (int): Width of the arrow elements.
+            scale_factor (int): Scaling factor applied to all plot dimensions.
         """
-        self.arrow_data = pd.read_csv(
-            config_manager.get_gencode_arrow_file(), sep="\t", compression="infer"
-        )
+        self.arrow_data = arrow_data
 
         # Extract colors:
         arrow_colors = config_manager.color_schema.arrow_colors
@@ -200,51 +201,75 @@ def __init__(
 
         # Extract other values
         self.chunk_size = config_manager.basic_parameters.chunk_size
-        self.pixel_size = config_manager.plot_parameters.pixel_size
-
-        self.arrow_width = arrow_width
+        self.pixel_size = config_manager.plot_parameters.pixel_size * scale_factor
+        logger.info(f"Pixel size: {self.pixel_size}")
 
-    def generate_arrow_polt(
-        self: GenerateArrowPlot, gene_name: str
-    ) -> tuple[str, float]:
+    @staticmethod
+    def _extract_arrow_data(
+        arrow_df: pd.DataFrame, gene_name: str, chunk_size: int, pixel_size: int
+    ) -> pd.DataFrame:
         """Generate arrow plot for a gene.
 
         Args:
+            arrow_df (pd.DataFrame):
             gene_name (str): Name of the gene.
+            chunk_size (int): Number of bp pooled together into one pixel
+            pixel_size (int): screen size of one pixel (chunk of dna)
 
-        Returns:
-            tuple[str, float]: SVG string and plot width.
+
+        Raises:
+            ValueError if gene not found in arrow file.
         """
         # Get CDS and UTR for a given gene:
         gene_df = (
-            self.arrow_data.loc[lambda df: df.gene_name == gene_name]
+            arrow_df.loc[lambda df: df.gene_name == gene_name]
             .sort_values("start")
             .reset_index(drop=True)
             .drop(["chr", "gene_name", "gene_id"], axis=1)
         )
 
         # If nothing found raise:
-        assert len(gene_df) > 1, f"Gene name ({gene_name}) was not found in the data."
+        if len(gene_df) == 0:
+            raise ValueError(
+                f"Gene name ({gene_name}) was not found in the arrow data."
+            )
+
+        # Initialise scaler:
+        scaler = Scaler(
+            gene_start=gene_df.start.min(),
+            chunk_size=chunk_size,
+            pixel_size=pixel_size,
+        )
 
         # Scaling genomic coordinates to screen coordinates:
-        gene_df = gene_df.assign(
-            relative_start=lambda row: (row["start"] - gene_df.start.min())
-            / self.chunk_size
-            * self.pixel_size,
-            relative_end=lambda row: (row["end"] - gene_df.start.min())
-            / self.chunk_size
-            * self.pixel_size,
-        ).assign(length=lambda row: row["relative_end"] - row["relative_start"])
-
-        # Calculate intron midpoints:
-        gene_df["next_start"] = gene_df.relative_start.drop(0).reset_index(drop=True)
-
-        gene_df["midpoint"] = (
-            gene_df.next_start - gene_df.relative_end
-        ) / 2 + gene_df.relative_end
-        self.df = gene_df.head()
+        return gene_df.assign(
+            relative_start=gene_df.start.apply(scaler.scale_genomic_coordinate),
+            relative_end=gene_df.end.apply(scaler.scale_genomic_coordinate),
+            length=lambda df: df.relative_end - df.relative_start,
+            next_start=lambda df: df.relative_start.drop(0).reset_index(drop=True),
+            midpoint=lambda df: (df.next_start - df.relative_end) / 2 + df.relative_end,
+        )
+
+    def generate_arrow_polt(
+        self: GenerateArrowPlot, gene_name: str
+    ) -> tuple[str, float]:
+        """Generate arrow plot.
+
+        Args:
+            gene_name (str): Name of the gene to be plotted.
 
+        Returns:
+            tuple[str, float]: SVG string and plot width.
+        """
         # Generate boxes:
+        gene_df = self._extract_arrow_data(
+            self.arrow_data, gene_name, self.chunk_size, self.pixel_size
+        )
+
+        # Store genomic bounds so generate_chunk_svg can use the same coordinate origin:
+        self._gene_genomic_start = int(gene_df["start"].min())
+        self._gene_genomic_end = int(gene_df["end"].max())
+
         boxes = gene_df.apply(self.draw_box, axis=1).dropna()
 
         # Generate lines connecting boxes:
@@ -259,9 +284,49 @@ def generate_arrow_polt(
 
         # Concatenate into single string:
         svg_string = "".join(lines.to_list() + boxes.to_list()) + arrow
-        # svg_object = svg_handler(svg_string, gene_df.relative_end.max(), self.arrow_width)
 
-        return svg_string, gene_df.relative_end.max()
+        # Add pixel_size to width so the arrowhead isn't clipped by the canvas edge:
+        return svg_string, gene_df.relative_end.max() + self.pixel_size
+
+    def generate_chunk_svg(
+        self: GenerateArrowPlot, genome_df: pd.DataFrame, extension: int = 10
+    ) -> str:
+        """Generate SVG rectangles for genome chunks overlapping the gene.
+
+        Must be called after generate_arrow_polt so that genomic bounds are set.
+
+        Args:
+            genome_df (pd.DataFrame): Integrated genome data with 'start', 'end',
+                and 'color' columns.
+            extension (int): Number of chunks to include beyond each end of the gene.
+
+        Returns:
+            str: SVG string of colored chunk rectangles.
+        """
+        scaler = Scaler(
+            gene_start=self._gene_genomic_start,
+            chunk_size=self.chunk_size,
+            pixel_size=self.pixel_size,
+        )
+
+        ext_bp = extension * self.chunk_size
+        chunks = genome_df.loc[
+            (genome_df["start"] < self._gene_genomic_end + ext_bp)
+            & (genome_df["end"] > self._gene_genomic_start - ext_bp)
+        ]
+
+        svg = ""
+        for _, row in chunks.iterrows():
+            x = scaler.scale_genomic_coordinate(row["start"])
+            width = round(
+                (row["end"] - row["start"]) / self.chunk_size * self.pixel_size
+            )
+            svg += (
+                f'<rect x="{x}" y="0" width="{width}" height="{self.pixel_size}"'
+                f' style="fill:{row["color"]}" />\n'
+            )
+
+        return svg
 
     def draw_arrow(self: GenerateArrowPlot, df: pd.DataFrame) -> str:
         """Draw an arrow for the gene structure.
@@ -272,7 +337,7 @@ def draw_arrow(self: GenerateArrowPlot, df: pd.DataFrame) -> str:
         Returns:
             str: SVG arrow string.
         """
-        arrow_width = self.arrow_width
+        arrow_width = self.pixel_size
 
         # Get orientation:
         row = df.iloc[0] if df.iloc[0]["strand"] == "-" else df.tail(1).iloc[0]
@@ -321,7 +386,7 @@ def draw_box(self: GenerateArrowPlot, row: pd.Series) -> str:
         return self.CHUNK_SVG.format(
             row["relative_start"],
             row["length"],
-            self.arrow_width,
+            self.pixel_size,
             self.line_color,
             fill_color,
         )
@@ -343,12 +408,12 @@ def draw_lines(self: GenerateArrowPlot, row: pd.Series) -> str | None:
             row["relative_end"],
             0,
             row["midpoint"],
-            -self.arrow_width / 2,
+            -self.pixel_size / 2,
             self.line_color,
         )
         connector += self.LINE_SVG.format(
             row["midpoint"],
-            -self.arrow_width / 2,
+            -self.pixel_size / 2,
             row["next_start"],
             0,
             self.line_color,
diff --git a/src/genome_plotter/functions/DataIntegrator.py b/src/genome_plotter/functions/DataIntegrator.py
index 411fd7c..d56e0dc 100644
--- a/src/genome_plotter/functions/DataIntegrator.py
+++ b/src/genome_plotter/functions/DataIntegrator.py
@@ -1,7 +1,3 @@
 """Module for integrating genomic data (deprecated - use input_parsers.data_integrator)."""
 
 from __future__ import annotations
-
-import logging
-
-logger = logging.getLogger(__name__)
diff --git a/src/genome_plotter/functions/GeneAnnotator.py b/src/genome_plotter/functions/GeneAnnotator.py
index e7145d4..c13d48a 100644
--- a/src/genome_plotter/functions/GeneAnnotator.py
+++ b/src/genome_plotter/functions/GeneAnnotator.py
@@ -2,9 +2,8 @@
 
 from __future__ import annotations
 
-import logging
-
 import pandas as pd
+from loguru import logger
 
 
 class PositionConverter:
@@ -76,7 +75,7 @@ def __init__(
         # Open gene file and store data:
         df = pd.read_csv(gene_file, sep="\t", compression="infer")
         self.__df = df.loc[df.chr == chromosome]
-        logging.info(
+        logger.info(
             "Adding annotation for {} genes on this chromosome.".format(len(self.__df))
         )
 
diff --git a/src/genome_plotter/input_parsers/data_integrator.py b/src/genome_plotter/input_parsers/data_integrator.py
index 9cf92d0..6e21880 100644
--- a/src/genome_plotter/input_parsers/data_integrator.py
+++ b/src/genome_plotter/input_parsers/data_integrator.py
@@ -2,19 +2,17 @@
 
 from __future__ import annotations
 
-import logging
 import pickle
 from typing import TYPE_CHECKING, Any
 
 import pandas as pd
 import pybedtools
+from loguru import logger
 
 if TYPE_CHECKING:
     from genome_plotter.functions.ColorFunctions import ColorPicker
 
 
-logger = logging.getLogger(__name__)
-
 
 def read_data(file: str, types: dict[str, Any]) -> pd.DataFrame:
     """Read the input data.
diff --git a/src/genome_plotter/input_parsers/fetch_cytobands.py b/src/genome_plotter/input_parsers/fetch_cytobands.py
index fab2825..28a0fe9 100644
--- a/src/genome_plotter/input_parsers/fetch_cytobands.py
+++ b/src/genome_plotter/input_parsers/fetch_cytobands.py
@@ -2,12 +2,9 @@
 
 from __future__ import annotations
 
-import logging
-
 import pandas as pd
 import requests
-
-logger = logging.getLogger(__name__)
+from loguru import logger
 
 
 # get cytoband data:
diff --git a/src/genome_plotter/input_parsers/fetch_ensembl.py b/src/genome_plotter/input_parsers/fetch_ensembl.py
index 775f743..99afca1 100644
--- a/src/genome_plotter/input_parsers/fetch_ensembl.py
+++ b/src/genome_plotter/input_parsers/fetch_ensembl.py
@@ -2,20 +2,18 @@
 
 from __future__ import annotations
 
-import logging
 import re
 from typing import TYPE_CHECKING
 
 import pandas as pd
 import requests
+from loguru import logger
 
 from genome_plotter.functions.FetchFromFtp import FetchFromFtp
 
 if TYPE_CHECKING:
     from genome_plotter.functions.ConfigManager import SourcePrototype
 
-logger = logging.getLogger(__name__)
-
 
 # get ensembl version
 def fetch_ensembl_version(url: str) -> int:
diff --git a/src/genome_plotter/input_parsers/fetch_gencode.py b/src/genome_plotter/input_parsers/fetch_gencode.py
index f412fbd..bad635e 100644
--- a/src/genome_plotter/input_parsers/fetch_gencode.py
+++ b/src/genome_plotter/input_parsers/fetch_gencode.py
@@ -2,19 +2,17 @@
 
 from __future__ import annotations
 
-import logging
 import re
 from typing import TYPE_CHECKING
 
 import pandas as pd
+from loguru import logger
 
 from genome_plotter.functions.FetchFromFtp import FetchFromFtp
 
 if TYPE_CHECKING:
     from genome_plotter.functions.ConfigManager import SourcePrototype
 
-logger = logging.getLogger(__name__)
-
 
 # Fetch and process Gencode data:
 class FetchGencode(FetchFromFtp):
diff --git a/src/genome_plotter/input_parsers/fetch_gwas_catalog.py b/src/genome_plotter/input_parsers/fetch_gwas_catalog.py
index 676c94e..9b2bb34 100644
--- a/src/genome_plotter/input_parsers/fetch_gwas_catalog.py
+++ b/src/genome_plotter/input_parsers/fetch_gwas_catalog.py
@@ -2,16 +2,15 @@
 
 from __future__ import annotations
 
-import logging
 from typing import TYPE_CHECKING
 
+from loguru import logger
+
 from genome_plotter.functions.FetchFromFtp import FetchFromFtp
 
 if TYPE_CHECKING:
     from genome_plotter.functions.ConfigManager import SourcePrototype
 
-logger = logging.getLogger(__name__)
-
 
 # Fetch GWAS Catalog data and parse:
 class FetchGwas(FetchFromFtp):
diff --git a/src/genome_plotter/logger_config.yaml b/src/genome_plotter/logger_config.yaml
deleted file mode 100644
index cc3d077..0000000
--- a/src/genome_plotter/logger_config.yaml
+++ /dev/null
@@ -1,25 +0,0 @@
-version: 1
-disable_existing_loggers: false
-formatters:
-  simple:
-    format: '%(asctime)s %(levelname)s %(module)s - %(funcName)s: %(message)s'
-    datefmt: '%Y-%m-%d %H:%M:%S'
-handlers:
-  console:
-    class: logging.StreamHandler
-    level: INFO
-    formatter: simple
-    stream: ext://sys.stdout
-  file:
-    class: logging.FileHandler
-    level: DEBUG
-    formatter: simple
-    filename: genome_plotter.log
-loggers:
-  simpleExample:
-    level: DEBUG
-    handlers: [console, file]
-    propagate: no
-root:
-  level: INFO
-  handlers: [console,file]
diff --git a/src/genome_plotter/plot_chromosome.py b/src/genome_plotter/plot_chromosome.py
index 7c2c286..dbe086a 100644
--- a/src/genome_plotter/plot_chromosome.py
+++ b/src/genome_plotter/plot_chromosome.py
@@ -4,13 +4,13 @@
 
 import argparse
 import json
-import logging.config
 import os
 from dataclasses import asdict
 
 import pandas as pd
-import yaml
+from loguru import logger
 
+from genome_plotter import LOG_FORMAT
 from genome_plotter.functions.ChromosomePlotter import ChromosomePlotter
 
 # Importing custom functions:
@@ -25,8 +25,6 @@
 from genome_plotter.functions.svg_handler import svg_handler
 from genome_plotter.input_parsers.data_integrator import DataIntegrator
 
-logger = logging.getLogger(__name__)
-
 
 def genes_annotation_wrapper(
     config_manager: Config, chromosome: str, height: int | float, gene_filename: str
@@ -317,12 +315,7 @@ def main() -> None:
     plot_folder = os.path.abspath(args.folder)
 
     # Initialise logger:
-    logger_config_path = os.path.join(os.path.dirname(__file__), "logger_config.yaml")
-    with open(logger_config_path, "r") as stream:
-        logger_config = yaml.safe_load(stream)
-
-    logging.config.dictConfig(logger_config)
-    logger = logging.getLogger(__name__)
+    logger.add("genome_plotter.log", level="DEBUG", format=LOG_FORMAT)
 
     # Reporting parameters:
     logger.info(f"Generating plot for chromosome: {chromosome}")
@@ -430,7 +423,7 @@ def main() -> None:
     chromosomeSvgObject.savePng(output_filename)
 
     if args.textFile:
-        logger.info(f'Saving svg file: {output_filename.replace("png","svg")}')
+        logger.info(f"Saving svg file: {output_filename.replace('png', 'svg')}")
         chromosomeSvgObject.saveSvg(output_filename.replace("png", "svg"))
 
     logger.info("All done.")
diff --git a/src/genome_plotter/plot_gene_arrow.py b/src/genome_plotter/plot_gene_arrow.py
new file mode 100644
index 0000000..55b3ede
--- /dev/null
+++ b/src/genome_plotter/plot_gene_arrow.py
@@ -0,0 +1,151 @@
+"""Plotting script for gene arrow diagrams."""
+
+from __future__ import annotations
+
+import argparse
+import json
+import os
+
+import pandas as pd
+from loguru import logger
+
+from genome_plotter import LOG_FORMAT
+from genome_plotter.functions.ColorFunctions import ColorPicker
+from genome_plotter.functions.ConfigManager import Config
+from genome_plotter.functions.CustomGenePlotter import (
+    CustomGeneIntegrator,
+    GenerateArrowPlot,
+)
+from genome_plotter.functions.svg_handler import svg_handler
+
+
+def parse_arguments() -> argparse.Namespace:
+    """Parse command line arguments.
+
+    Returns:
+        argparse.Namespace: Parsed arguments.
+    """
+    parser = argparse.ArgumentParser(
+        description="Generate an arrow plot (gene structure diagram) for a given gene. "
+        "See github: https://github.com/DSuveges/GenomePlotter"
+    )
+    parser.add_argument(
+        "-g",
+        "--gene",
+        help="Gene name (e.g. BRCA1)",
+        required=True,
+        type=str,
+    )
+    parser.add_argument(
+        "-d",
+        "--data_folder",
+        help="Path to the data folder containing processed files",
+        required=True,
+        type=str,
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        help="Path to config JSON file",
+        required=True,
+        type=str,
+    )
+    parser.add_argument(
+        "-o",
+        "--output",
+        help="Output file basename (defaults to {gene_name}_arrow)",
+        required=False,
+        type=str,
+        default=None,
+    )
+    parser.add_argument(
+        "-s",
+        "--scale-factor",
+        help="Scaling factor applied to all plot dimensions (default: 30)",
+        type=int,
+        default=30,
+    )
+
+    return parser.parse_args()
+
+
+def main() -> None:
+    """Entry point for the plot-gene-arrow CLI command."""
+    args = parse_arguments()
+
+    gene_name = args.gene
+    data_folder = os.path.abspath(args.data_folder)
+    config_file = args.config
+    output_basename = args.output if args.output else f"{gene_name}_arrow"
+    scale_factor = args.scale_factor
+
+    # Initialise logger:
+    logger.add("genome_plotter.log", level="DEBUG", format=LOG_FORMAT)
+
+    logger.info(f"Generating arrow plot for gene: {gene_name}")
+
+    # Initialise configuration:
+    with open(config_file) as f:
+        try:
+            config_manager = Config(**json.load(f))
+        except json.decoder.JSONDecodeError:
+            raise ValueError(
+                f"The provided config file ({config_file}) is not a valid JSON file."
+            )
+
+    # Set the data folder on the config:
+    config_manager.basic_parameters.data_folder = data_folder
+
+    # Generate arrow plot:
+    logger.info("Initializing arrow plot generator.")
+    arrow_plotter = GenerateArrowPlot(
+        pd.read_csv(
+            config_manager.get_gencode_arrow_file(), sep="\t", compression="infer"
+        ),
+        config_manager,
+        scale_factor=scale_factor,
+    )
+
+    logger.info(f"Generating arrow plot for gene: {gene_name}")
+    svg_arrow, width = arrow_plotter.generate_arrow_polt(gene_name)
+
+    # Integrate genome chunk data and generate the chunk layer:
+    logger.info("Integrating genome chunk data.")
+    color_picker = ColorPicker(
+        config_manager.color_schema.chromosome_colors, count=30
+    )
+    integrator = CustomGeneIntegrator(gene_name, config_manager)
+    integrator.integrate(color_picker)
+    chunk_extension = 10
+    svg_chunks = arrow_plotter.generate_chunk_svg(
+        integrator.get_integrated_data(), extension=chunk_extension
+    )
+
+    # Layout: chunk layer on top, arrow below with a gap equal to one pixel_size:
+    px = arrow_plotter.pixel_size
+    gap = px
+    arrow_y_offset = px + gap
+    svg_arrow_shifted = f'<g transform="translate(0 {arrow_y_offset})">\n{svg_arrow}\n</g>\n'
+
+    # The extension adds extra chunks left and right of the gene; expand canvas accordingly.
+    # Left extension is handled by shifting translate_x so negative-x chunks land inside the canvas.
+    extension_px = chunk_extension * px
+    canvas_height = arrow_y_offset + px * 3
+    svg_obj = svg_handler(svg_chunks + svg_arrow_shifted, width + extension_px, canvas_height)
+    svg_obj.group(translate=(px + extension_px, px))
+
+    # Save as SVG and PNG:
+    svg_filename = f"{output_basename}.svg"
+    png_filename = f"{output_basename}.png"
+
+    logger.info(f"Saving SVG: {svg_filename}")
+    svg_obj.saveSvg(svg_filename)
+
+    logger.info(f"Saving PNG: {png_filename}")
+    svg_obj.savePng(png_filename)
+
+    logger.info("All done.")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/src/genome_plotter/prepare_data.py b/src/genome_plotter/prepare_data.py
index 5256aea..0d77e1d 100644
--- a/src/genome_plotter/prepare_data.py
+++ b/src/genome_plotter/prepare_data.py
@@ -4,11 +4,11 @@
 
 import argparse
 import json
-import logging.config
 import os
 
-import yaml
+from loguru import logger
 
+from genome_plotter import LOG_FORMAT
 from genome_plotter.functions.ConfigManager import Config
 from genome_plotter.input_parsers.data_integrator import integrate_data
 from genome_plotter.input_parsers.fetch_cytobands import FetchCytobands
@@ -19,8 +19,6 @@
 from genome_plotter.input_parsers.fetch_gencode import FetchGencode
 from genome_plotter.input_parsers.fetch_gwas_catalog import FetchGwas
 
-logger = logging.getLogger(__name__)
-
 
 def parse_args() -> argparse.Namespace:
     """Parse command line arguments.
@@ -118,7 +116,7 @@ def run(configuration: Config) -> None:
     )
 
     # Fetching GENCODE data:
-    logging.info("Fetching GENCODE data.")
+    logger.info("Fetching GENCODE data.")
     gencode_retrieve = FetchGencode(configuration.source_data.gencode_data)
     gencode_retrieve.retrieve_data()
     gencode_retrieve.process_gencode_data()
@@ -186,12 +184,7 @@ def main() -> None:
     args = parse_args()
 
     # Initialise logger:
-    logger_config_path = os.path.join(os.path.dirname(__file__), "logger_config.yaml")
-    with open(logger_config_path, "r") as stream:
-        logger_config = yaml.safe_load(stream)
-
-    logging.config.dictConfig(logger_config)
-    logger = logging.getLogger(__name__)
+    logger.add("genome_plotter.log", level="DEBUG", format=LOG_FORMAT)
 
     # Resolve config file: use bundled default if not provided:
     if args.config is None:
diff --git a/uv.lock b/uv.lock
index 7664c9d..7591211 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,5 +1,5 @@
 version = 1
-revision = 3
+revision = 2
 requires-python = ">=3.12"
 resolution-markers = [
     "python_full_version >= '3.14' and sys_platform == 'win32'",
@@ -58,11 +58,11 @@ wheels = [
 
 [[package]]
 name = "certifi"
-version = "2026.1.4"
+version = "2026.2.25"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/e0/2d/a891ca51311197f6ad14a7ef42e2399f36cf2f9bd44752b3dc4eab60fdc5/certifi-2026.1.4.tar.gz", hash = "sha256:ac726dd470482006e014ad384921ed6438c457018f4b3d204aea4281258b2120", size = 154268, upload-time = "2026-01-04T02:42:41.825Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/af/2d/7bf41579a8986e348fa033a31cdd0e4121114f6bce2457e8876010b092dd/certifi-2026.2.25.tar.gz", hash = "sha256:e887ab5cee78ea814d3472169153c2d12cd43b14bd03329a39a9c6e2e80bfba7", size = 155029, upload-time = "2026-02-25T02:54:17.342Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/e6/ad/3cc14f097111b4de0040c83a525973216457bbeeb63739ef1ed275c1c021/certifi-2026.1.4-py3-none-any.whl", hash = "sha256:9943707519e4add1115f44c2bc244f782c0249876bf51b6599fee1ffbedd685c", size = 152900, upload-time = "2026-01-04T02:42:40.15Z" },
+    { url = "https://files.pythonhosted.org/packages/9a/3c/c17fb3ca2d9c3acff52e30b309f538586f9f5b9c9cf454f3845fc9af4881/certifi-2026.2.25-py3-none-any.whl", hash = "sha256:027692e4402ad994f1c42e52a4997a9763c646b73e4096e4d5d6db8af1d6f0fa", size = 153684, upload-time = "2026-02-25T02:54:15.766Z" },
 ]
 
 [[package]]
@@ -133,59 +133,75 @@ wheels = [
 
 [[package]]
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-version = "3.4.4"
-source = { registry = "https://pypi.org/simple" }
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