kitikiplot 0.2.1__tar.gz → 0.2.3__tar.gz

{kitikiplot-0.2.1 → kitikiplot-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: kitikiplot
-Version: 0.2.1
+Version: 0.2.3
 Summary: A Python library to visualize categorical sliding window data.
 License: MIT
 Keywords: sliding window,sequential,time-series,genome,categorical data
@@ -14,6 +14,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Dist: biopython (>=1.85)
 Requires-Dist: matplotlib (>=3.10.1)
 Requires-Dist: numpy (>=2.2.5)
 Requires-Dist: pandas (>=2.2.3)
@@ -82,11 +83,11 @@ ktk.plot( display_legend= True ) # Display the legend
 Check out the complete <b>guide of customization</b> [here](https://github.com/BodduSriPavan-111/kitikiplot/blob/main/examples/Usage_Guide.ipynb).
 
 ## To-do
+🟢 Domain-specific modules (In Progress) </br>
 🟢 Streamlit Demo Interface (In Progress) </br>
 🟢 Website for documentation (In Progress)
 - [ ] Tooltip
 - [ ] Interactive Plot
-- [ ] Domain-specific modules
 
 Please refer <a href="https://github.com/BodduSriPavan-111/kitikiplot/blob/main/CONTRIBUTING.md">CONTRIBUTING.md</a> for <b>contributions</b> to kitikiplot.
 

{kitikiplot-0.2.1 → kitikiplot-0.2.3}/README.md

@@ -57,11 +57,11 @@ ktk.plot( display_legend= True ) # Display the legend
 Check out the complete <b>guide of customization</b> [here](https://github.com/BodduSriPavan-111/kitikiplot/blob/main/examples/Usage_Guide.ipynb).
 
 ## To-do
+🟢 Domain-specific modules (In Progress) </br>
 🟢 Streamlit Demo Interface (In Progress) </br>
 🟢 Website for documentation (In Progress)
 - [ ] Tooltip
 - [ ] Interactive Plot
-- [ ] Domain-specific modules
 
 Please refer <a href="https://github.com/BodduSriPavan-111/kitikiplot/blob/main/CONTRIBUTING.md">CONTRIBUTING.md</a> for <b>contributions</b> to kitikiplot.
 

kitikiplot-0.2.3/kitikiplot/genomics/grid.py

@@ -0,0 +1,54 @@
+"""
+File Name: linear.py
+Description: This file defines linear genomic plot
+Author: Boddu Sri Pavan
+Date Created: 21-05-2025
+Last Modified: 24-05-2025
+"""
+
+from kitikiplot.core import KitikiPlot
+
+import pandas as pd
+
+def plot( nucleotide_sequence: str, window_length= 30, cell_width= 2 ):
+    """
+    Generates linear genomic plot for short genome sequences.
+
+    Parameters
+    ----------
+    nucleotide_sequence : str
+        - Sequence of 'A', 'T', 'G', and 'C'.
+    """
+
+    # Preprocess input genomic sequence
+    nucleotide_sequence=nucleotide_sequence.upper()
+
+    residual= len(nucleotide_sequence)%window_length
+
+    l= []
+    for index in range( len(nucleotide_sequence)// window_length):
+
+        l.append( list(nucleotide_sequence[index*window_length: (index+1)*window_length]) )
+
+    if residual > 0:
+        l.append( list(nucleotide_sequence[(-1)*residual:]) + ["No_Data"]* (window_length- residual) )
+
+    grid_df= pd.DataFrame(l)
+
+    ktk= KitikiPlot( data= grid_df, stride= 0 )
+
+    ktk.plot(
+                figsize= (grid_df.shape[1]//3, grid_df.shape[0]//3),
+                cell_width= cell_width,
+                cmap= {'A': '#007FFF', 'T': "#fffc00", "G": "#00ff00", "C": "#960018"},
+                transpose= True,
+                window_gap= 0,
+                xlabel= "Nucleotides",
+                ylabel= "Nucleotide Chunk",
+                display_xticks= False,
+                display_yticks= False,
+                title= "Grid Plot: Nucleotide Sequence Visualization",
+                display_legend= True,
+                legend_kwargs= {"bbox_to_anchor": (1.01, 1), "loc":'upper left', "borderaxespad": 0.},
+                kitiki_cell_kwargs= {"linewidth": 0.5}
+            )

kitikiplot-0.2.3/kitikiplot/genomics/linear.py

@@ -0,0 +1,39 @@
+"""
+File Name: linear.py
+Description: This file defines linear genomic plot
+Author: Boddu Sri Pavan
+Date Created: 21-05-2025
+Last Modified: 24-05-2025
+"""
+
+from kitikiplot.core import KitikiPlot
+
+def plot( nucleotide_sequence: str )->  bool:
+    """
+    Generates linear genomic plot for short genome sequences.
+
+    Parameters
+    ----------
+    nucleotide_sequence : str
+        - Sequence of 'A', 'T', 'G', and 'C'.
+    """
+
+    # Preprocess input genomic sequence
+    nucleotide_sequence=nucleotide_sequence.upper()
+
+    ktk= KitikiPlot( data= nucleotide_sequence, stride= 1, window_length= len(nucleotide_sequence) )
+
+    ktk.plot(
+                figsize= (20, 1),
+                cell_width= 2,
+                cmap= {'A': '#007FFF', 'T': "#fffc00", "G": "#00ff00", "C": "#960018"},
+                transpose= True,
+                xlabel= "Nucleotides",
+                ylabel= "Window",
+                display_yticks= False,
+                xtick_prefix= "Nucleotide",
+                xticks_rotation= 90,
+                title= "Linear Plot: Nucleotide Sequence Visualization",
+                display_legend= True,
+                legend_kwargs= {"bbox_to_anchor": (1.01, 1), "loc":'upper left', "borderaxespad": 0.}
+            )

{kitikiplot-0.2.1 → kitikiplot-0.2.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "kitikiplot"
-version = "0.2.1"
+version = "0.2.3"
 description = "A Python library to visualize categorical sliding window data."
 authors = ["Boddu Sri Pavan <boddusripavan111@gmail.com>"]
 readme = "README.md"
@@ -28,3 +28,4 @@ python = ">=3.11"  # You may want to adjust this minimum version requirement
 numpy = ">=2.2.5"
 pandas = ">=2.2.3"
 matplotlib = ">=3.10.1"
+biopython = ">=1.85"