Enhance x-tick label customization: add font size, color, and rotatio…

.gitignore

@@ -189,3 +189,8 @@ examples/new_test_examples/*
 
 # Ignore new tools examples
 examples/new_tools/
+
+
+#ignore test output data
+output*
+*output

ProtPeptigram/DataProcessor.py

@@ -75,14 +75,15 @@ def load_peaks_data(self, file_path: str) -> pd.DataFrame:
         try:
             self.peaks_data = pd.read_csv(file_path)
             console.log(f"Loaded {len(self.peaks_data)} peptide entries from {file_path}", style="bold green")
-
+            self.peaks_data = self.peaks_data.rename(columns=lambda x: str(x).capitalize())
             # Check required columns
             required_cols = ['Peptide', 'Accession']
             missing_cols = [col for col in required_cols if col not in self.peaks_data.columns]
 
             if missing_cols:
                 raise ValueError(f"Missing required columns: {', '.join(missing_cols)}")
-
+
+
             # Find intensity columns
             self.intensity_cols = [col for col in self.peaks_data.columns if col.startswith(self.sample_prefix)]
 
@@ -281,7 +282,7 @@ def filter_and_format_data(self,
         formatted_rows = []
 
         # Extract sample names from intensity columns
-        sample_names = [col.replace(self.sample_prefix, '') for col in self.intensity_cols]
+        sample_names = [re.sub(r'^[_\-\*]+', '', col.replace(self.sample_prefix, '')) for col in self.intensity_cols]
 
         # Process each peptide
         for _, row in data.iterrows():

ProtPeptigram/__init__.py

@@ -23,6 +23,6 @@
 #controll for __all__ to limit what is imported when using 'from module import *'
 # __all__ = ['PeptideDataProcessor', 'ImmunoViz']
 
-__version__ = "1.0.1-dev"
+__version__ = "1.1.0-dev"
 __author__ = "Sanjay Krishna,Prithvi Munday,Chen Li"
 __email__ = "sanjay.sondekoppagopalakrishna@monash.edu"

ProtPeptigram/runner.py

@@ -106,7 +106,6 @@ def run_pipeline(
         Intensity threshold for filtering peptides (default: 0.0)
     min_samples : int, optional
         Minimum number of samples a peptide must be present in (default: 1)
-
     Returns:
     --------
     tuple: (PeptideDataProcessor, ImmunoViz) - The processor and visualization objects
@@ -187,11 +186,13 @@ def run_pipeline(
                 title=f"Peptide-Protein alignment visualisation - {prot}",
                 color_by_protein_and_intensity=False,
                 intensity_cmaps=["Blues", "Reds", "Greens", "Purples"],
-                protein_cmap="Set1",
+                protein_cmap="Set1", 
                 external_legend=True,
                 highlight=True,
                 auto_highlight=True,
                 highlight_alpha=0.3,
+                use_sample_color_bars=True,
+                sample_bar_width=6,
                 dpi=120
             )
 

__init__.py

@@ -1 +1,17 @@
-# import peptigram
+# import peptigram
+# ProtPeptigram/__init__.py
+# import sys
+# import os
+
+# # Add the parent directory to the path so we can import main.py from root
+# sys.path.insert(0, os.path.dirname(os.path.dirname(__file__)))
+
+# try:
+#     from main import main
+# except ImportError:
+#     # If main.py is not in root, define a placeholder
+#     def main():
+#         print("Main function not found")
+#         return 1
+
+# __all__ = ['main']

data/JCI146771_Mouse_peptides_peaks_online.csv

@@ -1,4 +1,4 @@
-Peptide,-10lgP,Mass,Length,ppm,m/z,RT,Accession,PTM,AScore,Area Sample 16,Intensity_Hep_B10BR_28-14-8s,Intensity_Hep_B10BR_K9-178,Intensity_178-3 skin graft_28-14-8s,Intensity_178-3 skin graft_K9-178,Intensity_178-3 spleen_K9-178,Intensity_178-3 spleen_Y-3
+Peptide,-10lgP,Mass,Length,ppm,m/z,RT,Accession,PTM,AScore,Area Sample 16,Intensity_Hep_B10BR_28-14-8s,intensity_Hep_B10BR_K9-178,Intensity_178-3 skin graft_28-14-8s,Intensity_178-3 skin graft_K9-178,Intensity_178-3 spleen_K9-178,Intensity_178-3 spleen_Y-3
 TPVITGAPYEYR,55.75,1365.6929,12,-0.6,683.8533,41.7,i#CONTAM#RT-pepF,,,9.94E+08,6.10E+08,6.70E+08,7.41E+08,7.53E+08,1.26E+09,7.62E+08
 YILAGVENSK,49.2,1092.5815,10,0.4,1093.5892,35.74,i#CONTAM#RT-pepD,,,5.77E+08,5.92E+08,5.10E+08,4.62E+08,5.66E+08,9.02E+08,7.54E+08
 GTFIIDPGGVIR,50.91,1243.6924,12,0.6,415.5717,57.95,i#CONTAM#RT-pepI,,,4.77E+08,3.35E+08,3.56E+08,4.68E+08,5.75E+08,8.92E+08,3.69E+08