kitikiplot 0.2.2__tar.gz → 0.2.3__tar.gz

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Files changed (11) hide show
  1. {kitikiplot-0.2.2 → kitikiplot-0.2.3}/PKG-INFO +2 -2
  2. {kitikiplot-0.2.2 → kitikiplot-0.2.3}/README.md +1 -1
  3. kitikiplot-0.2.3/kitikiplot/genomics/grid.py +54 -0
  4. {kitikiplot-0.2.2 → kitikiplot-0.2.3}/kitikiplot/genomics/linear.py +2 -4
  5. {kitikiplot-0.2.2 → kitikiplot-0.2.3}/pyproject.toml +1 -1
  6. {kitikiplot-0.2.2 → kitikiplot-0.2.3}/LICENSE +0 -0
  7. {kitikiplot-0.2.2 → kitikiplot-0.2.3}/kitikiplot/core/__init__.py +0 -0
  8. {kitikiplot-0.2.2 → kitikiplot-0.2.3}/kitikiplot/core/kitiki_cell.py +0 -0
  9. {kitikiplot-0.2.2 → kitikiplot-0.2.3}/kitikiplot/core/kitiki_color_config.py +0 -0
  10. {kitikiplot-0.2.2 → kitikiplot-0.2.3}/kitikiplot/core/kitikiplot.py +0 -0
  11. {kitikiplot-0.2.2 → kitikiplot-0.2.3}/kitikiplot/genomics/__init__.py +0 -0
{kitikiplot-0.2.2 → kitikiplot-0.2.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: kitikiplot
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- Version: 0.2.2
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+ Version: 0.2.3
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  Summary: A Python library to visualize categorical sliding window data.
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  License: MIT
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  Keywords: sliding window,sequential,time-series,genome,categorical data
@@ -83,11 +83,11 @@ ktk.plot( display_legend= True ) # Display the legend
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  Check out the complete <b>guide of customization</b> [here](https://github.com/BodduSriPavan-111/kitikiplot/blob/main/examples/Usage_Guide.ipynb).
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  ## To-do
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+ 🟢 Domain-specific modules (In Progress) </br>
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  🟢 Streamlit Demo Interface (In Progress) </br>
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  🟢 Website for documentation (In Progress)
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  - [ ] Tooltip
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  - [ ] Interactive Plot
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- - [ ] Domain-specific modules
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  Please refer <a href="https://github.com/BodduSriPavan-111/kitikiplot/blob/main/CONTRIBUTING.md">CONTRIBUTING.md</a> for <b>contributions</b> to kitikiplot.
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{kitikiplot-0.2.2 → kitikiplot-0.2.3}/README.md RENAMED
@@ -57,11 +57,11 @@ ktk.plot( display_legend= True ) # Display the legend
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  Check out the complete <b>guide of customization</b> [here](https://github.com/BodduSriPavan-111/kitikiplot/blob/main/examples/Usage_Guide.ipynb).
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  ## To-do
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+ 🟢 Domain-specific modules (In Progress) </br>
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  🟢 Streamlit Demo Interface (In Progress) </br>
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  🟢 Website for documentation (In Progress)
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  - [ ] Tooltip
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  - [ ] Interactive Plot
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- - [ ] Domain-specific modules
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  Please refer <a href="https://github.com/BodduSriPavan-111/kitikiplot/blob/main/CONTRIBUTING.md">CONTRIBUTING.md</a> for <b>contributions</b> to kitikiplot.
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kitikiplot-0.2.3/kitikiplot/genomics/grid.py ADDED
@@ -0,0 +1,54 @@
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+ """
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+ File Name: linear.py
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+ Description: This file defines linear genomic plot
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+ Author: Boddu Sri Pavan
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+ Date Created: 21-05-2025
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+ Last Modified: 24-05-2025
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+ """
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+
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+ from kitikiplot.core import KitikiPlot
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+
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+ import pandas as pd
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+
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+ def plot( nucleotide_sequence: str, window_length= 30, cell_width= 2 ):
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+ """
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+ Generates linear genomic plot for short genome sequences.
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+
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+ Parameters
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+ ----------
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+ nucleotide_sequence : str
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+ - Sequence of 'A', 'T', 'G', and 'C'.
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+ """
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+
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+ # Preprocess input genomic sequence
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+ nucleotide_sequence=nucleotide_sequence.upper()
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+
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+ residual= len(nucleotide_sequence)%window_length
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+
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+ l= []
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+ for index in range( len(nucleotide_sequence)// window_length):
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+
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+ l.append( list(nucleotide_sequence[index*window_length: (index+1)*window_length]) )
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+
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+ if residual > 0:
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+ l.append( list(nucleotide_sequence[(-1)*residual:]) + ["No_Data"]* (window_length- residual) )
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+
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+ grid_df= pd.DataFrame(l)
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+
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+ ktk= KitikiPlot( data= grid_df, stride= 0 )
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+
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+ ktk.plot(
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+ figsize= (grid_df.shape[1]//3, grid_df.shape[0]//3),
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+ cell_width= cell_width,
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+ cmap= {'A': '#007FFF', 'T': "#fffc00", "G": "#00ff00", "C": "#960018"},
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+ transpose= True,
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+ window_gap= 0,
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+ xlabel= "Nucleotides",
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+ ylabel= "Nucleotide Chunk",
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+ display_xticks= False,
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+ display_yticks= False,
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+ title= "Grid Plot: Nucleotide Sequence Visualization",
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+ display_legend= True,
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+ legend_kwargs= {"bbox_to_anchor": (1.01, 1), "loc":'upper left', "borderaxespad": 0.},
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+ kitiki_cell_kwargs= {"linewidth": 0.5}
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+ )
{kitikiplot-0.2.2 → kitikiplot-0.2.3}/kitikiplot/genomics/linear.py RENAMED
@@ -3,13 +3,11 @@ File Name: linear.py
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  Description: This file defines linear genomic plot
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  Author: Boddu Sri Pavan
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  Date Created: 21-05-2025
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- Last Modified: 21-05-2025
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+ Last Modified: 24-05-2025
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  """
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  from kitikiplot.core import KitikiPlot
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- from Bio import SeqIO
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-
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  def plot( nucleotide_sequence: str )-> bool:
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  """
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  Generates linear genomic plot for short genome sequences.
@@ -35,7 +33,7 @@ def plot( nucleotide_sequence: str )-> bool:
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  display_yticks= False,
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  xtick_prefix= "Nucleotide",
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  xticks_rotation= 90,
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- title= "Genome Visualization",
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+ title= "Linear Plot: Nucleotide Sequence Visualization",
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  display_legend= True,
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  legend_kwargs= {"bbox_to_anchor": (1.01, 1), "loc":'upper left', "borderaxespad": 0.}
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  )
{kitikiplot-0.2.2 → kitikiplot-0.2.3}/pyproject.toml RENAMED
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  [tool.poetry]
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  name = "kitikiplot"
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- version = "0.2.2"
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+ version = "0.2.3"
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  description = "A Python library to visualize categorical sliding window data."
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  authors = ["Boddu Sri Pavan <boddusripavan111@gmail.com>"]
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  readme = "README.md"
{kitikiplot-0.2.2 → kitikiplot-0.2.3}/LICENSE RENAMED
File without changes