kitikiplot 0.2.8__py3-none-any.whl → 1.0.0__py3-none-any.whl

kitikiplot/core/kitiki_cell.py

@@ -161,10 +161,12 @@ class KitikiCell(ColorConfig):
 
                 max_y= cell_height*(self.cols-1)+ ((self.rows)*self.stride*cell_height)
 
-                if (focus_dim_y > max_y - (cell_height*self.window_length + cell_height*x*self.stride)) and  (focus_dim_y <= max_y - (cell_height*x*self.stride)):
-                    kitiki_cell_kwargs["alpha"]= 1
-                else:
-                    kitiki_cell_kwargs["alpha"]= focus_alpha
+                if kitiki_cell_kwargs.get("alpha", None) == None:
+
+                    if (focus_dim_y > max_y - (cell_height*self.window_length + cell_height*x*self.stride)) and  (focus_dim_y <= max_y - (cell_height*x*self.stride)):
+                        kitiki_cell_kwargs["alpha"]= 1
+                    else:
+                        kitiki_cell_kwargs["alpha"]= focus_alpha
 
         # Adjust dimensions if 'transpose' is set to 'True'
         else:
@@ -188,10 +190,12 @@ class KitikiCell(ColorConfig):
                 min_dim_x= cell_height + align_factor
                 max_dim_x= cell_height*(self.cols)+ align_factor
 
-                if (min_dim_x <= dim_x) and (dim_x <= max_dim_x):
-                    kitiki_cell_kwargs["alpha"]= 1
-                else:
-                    kitiki_cell_kwargs["alpha"]= focus_alpha
+                if  kitiki_cell_kwargs.get("alpha", None) == None:
+
+                    if (min_dim_x <= dim_x) and (dim_x <= max_dim_x):
+                        kitiki_cell_kwargs["alpha"]= 1
+                    else:
+                        kitiki_cell_kwargs["alpha"]= focus_alpha
 
 
         # Clean up all local variables for efficient memory management

kitikiplot/core/kitikiplot.py

@@ -198,6 +198,9 @@ class KitikiPlot(KitikiCell):
         legend_hatch : bool (optional)
             - A flag indicating whether to include hatch patterns in the legend. 
             - Default is False.
+        return_figure: bool (optional) 
+            - A flag indicating whether to return plot.
+            - Default is False.
         legend_kwargs : dict (optional)
             - Additional keyword arguments passed to customize the legend.
             - Default is {}.
@@ -246,13 +249,13 @@ class KitikiPlot(KitikiCell):
             # This allows for plotting only a subset of the data based on the user-defined range
             window_range= range( window_range[0], window_range[1])
 
+        each_sample= np.concatenate( (data[0], data[1:data.shape[0], (-1)*self.stride:].flatten()) )
+
         if focus != None:
-            col_range= self.rows + self.window_length - 1
+            col_range= (self.rows * self.stride) + self.window_length - self.stride
         else:
             col_range= self.cols
 
-        each_sample= np.concatenate( (data[0], data[1:data.shape[0], (-1)*self.stride:].flatten()) )
-
         # Generate cells for each sample in the specified window range and time frame columns
         for index in window_range:
 
@@ -262,9 +265,9 @@ class KitikiPlot(KitikiCell):
             for time_frame in range( col_range ):
                 
                 if type(focus) != bool:
-
+                    
                     kitiki_cell_kwargs["alpha"]= focus_alpha if focus != None and ( time_frame< focus[0] or time_frame>= focus[1] ) else 1
-                
+
                 # Create each cell using specified parameters and add it to patches list 
                 cell_gen= self.create(  x= index,
                                         y= time_frame,
@@ -295,7 +298,9 @@ class KitikiPlot(KitikiCell):
             # Calculate x and y positions for ticks when not transposed
             x_positions= [(i+1)*window_gap+(i+1)*cell_width+cell_width/2 for i in range(self.rows)]
             
-            y_positions= [(self.rows+ self.cols- self.stride- i)*cell_height+cell_height/2 for i in range(self.stride*self.rows+self.cols)]
+            # y_positions= [(self.rows+ self.cols- self.stride- i)*cell_height+cell_height/2 for i in range(self.stride*self.rows+self.cols)]
+            
+            y_positions= [cell_height*(self.cols-i-1)+ self.rows*self.stride*cell_height + cell_height/2  for i in range(col_range)]
 
             # Display xticks if 'display_xticks' is True
             if display_xticks:
@@ -333,9 +338,9 @@ class KitikiPlot(KitikiCell):
 
                 # Configure default yticks
                 else:
-
+                    
                     # Set y-ticks with appropriate labels and rotation
-                    plt.yticks( y_positions, [ytick_prefix+"_"+str(i) for i in range(self.stride*self.rows+self.cols)], rotation= yticks_rotation)
+                    plt.yticks( y_positions, [ytick_prefix+"_"+str(i) for i in range(col_range)], rotation= yticks_rotation)
             
             # Else turn off the yticks
             else:

kitikiplot/ecology/grid.py

@@ -0,0 +1,54 @@
+"""
+File Name: linear.py
+Description: This file defines grid concentration plot for ecological data visualization
+Author: Boddu Sri Pavan
+Date Created: 31-05-2025
+Last Modified: 31-05-2025
+"""
+
+from kitikiplot.core import KitikiPlot
+
+def plot( data, stride, window_length,
+            cmap= {},
+            figsize= (20, 5),
+            focus= True,
+            focus_alpha= 0.2,
+            transpose= True,
+            align= False,
+            xlabel= "Time",
+            ylabel= "Sliding Windows of CO(GT) values (in mg/m^3)",
+            display_xticks= True,
+            xticks_values= [],
+            yticks_values= [],
+            ytick_prefix= "Window",
+            xticks_rotation= 90, 
+            display_legend= True,
+            title= "CO(GT) Trend in Air",
+            legend_kwargs= {"bbox_to_anchor": (1.01, 1), "loc":'upper left', "borderaxespad": 0.}
+        ):
+    """
+    Grid Plot for ecological data.
+    Focus can be set to highlight particular time-interval of sliding window.
+    """
+
+    ktk= KitikiPlot( data= data, stride= stride, window_length= window_length )
+
+    ktk.plot(
+        figsize= (20, 5),
+        cell_width= 2,
+        cmap= cmap,
+        focus= focus,
+        focus_alpha= focus_alpha,
+        transpose= transpose,
+        align= align,
+        xlabel= xlabel,
+        ylabel= ylabel,
+        display_xticks= display_xticks,
+        xticks_values= xticks_values,
+        yticks_values= yticks_values,
+        ytick_prefix= ytick_prefix,
+        xticks_rotation= xticks_rotation, 
+        display_legend= display_legend,
+        title= title,
+        legend_kwargs= legend_kwargs
+    )

kitikiplot/ecology/linear.py

@@ -8,23 +8,41 @@ Last Modified: 25-05-2025
 
 from kitikiplot.core import KitikiPlot
 
-def plot( data, focus, focus_alpha, xlabel, ylabel, xticks_values, ytick_prefix, cmap= {} ):
-
-    ktk= KitikiPlot( data= data, stride= 1, window_length= len(data) )
+def plot( 
+            data, focus, focus_alpha, xlabel, ylabel, xticks_values, ytick_prefix, 
+            stride= 1,
+            figsize= (20,1), 
+            cell_width= 2, 
+            transpose= True, 
+            display_xticks= True, 
+            xticks_rotation= 90,
+            display_legend= True, 
+            title= "Linear Plot: Ecology Data Visualization", 
+            return_figure= True, 
+            legend_kwargs= {"bbox_to_anchor": (1.01, 1), "loc":'upper left', "borderaxespad": 0.},
+            cmap= {} 
+        ):
+    """
+    Linear Plot for ecological data.
+    Focus can be set to highlight particular time-interval
+    """
+    
+    ktk= KitikiPlot( data= data, stride= stride, window_length= len(data) )
 
     ktk.plot(
-            figsize= (20, 1),
-            cell_width= 2,
+            figsize= figsize,
+            cell_width= cell_width,
             cmap= cmap,
             focus= focus,
             focus_alpha= focus_alpha,
-            transpose= True,
+            transpose= transpose,
             xlabel= xlabel,
             ylabel= ylabel,
-            display_xticks= True,
+            display_xticks= display_xticks,
             xticks_values= xticks_values,
             ytick_prefix= ytick_prefix,
-            xticks_rotation= 90, 
-            display_legend= True,
-            title= "Linear Plot: Ecology Data Visualization",
-            legend_kwargs= {"bbox_to_anchor": (1.01, 1), "loc":'upper left', "borderaxespad": 0.})
+            xticks_rotation= xticks_rotation, 
+            display_legend= display_legend,
+            title= title,
+            return_figure= return_figure,
+            legend_kwargs= legend_kwargs)

kitikiplot/genomics/grid.py

@@ -12,7 +12,7 @@ import pandas as pd
 
 def plot( nucleotide_sequence: str, window_length= 30, cell_width= 2 ):
     """
-    Generates linear genomic plot for short genome sequences.
+    Generates grid genomic plot for short genome sequences.
 
     Parameters
     ----------

{kitikiplot-0.2.8.dist-info → kitikiplot-1.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: kitikiplot
-Version: 0.2.8
+Version: 1.0.0
 Summary: A Python library to visualize categorical sliding window data.
 License: MIT
 Keywords: sliding window,sequential,time-series,genome,categorical data
@@ -14,10 +14,10 @@ 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)
+Requires-Dist: biopython
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
 Project-URL: Bug Tracker, https://github.com/BodduSriPavan-111/kitikiplot/issues
 Project-URL: Documentation, https://github.com/BodduSriPavan-111/kitikiplot/wiki
 Project-URL: Repository, https://github.com/BodduSriPavan-111/kitikiplot

kitikiplot-1.0.0.dist-info/RECORD

@@ -0,0 +1,13 @@
+kitikiplot/core/__init__.py,sha256=7LpJy1V-PZ-JlfjsnRMjMXxTKaFt0JP0mj-A0SgS-sE,34
+kitikiplot/core/kitiki_cell.py,sha256=acYIsPw-WW75OXq7dw5b6NJ9gn6eM7sSc70OHwbitVg,8536
+kitikiplot/core/kitiki_color_config.py,sha256=yOWnJNoYo1BN7UMGTFgc8zpMljBbNpFDLLq7JZF3ATE,11857
+kitikiplot/core/kitikiplot.py,sha256=eDW8-urInxpdFrViPk8CDk9eOt9uLbDHRH9ggzwHxeQ,21144
+kitikiplot/ecology/grid.py,sha256=DdXyu2B4IGLADG5a20go17AMXG6Iv93wKQdG-SQ-_Ik,1684
+kitikiplot/ecology/linear.py,sha256=RmpIHQvETL0a6GN2cUHlQd0VXbE0hepojG0NxQIVca8,1565
+kitikiplot/genomics/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+kitikiplot/genomics/grid.py,sha256=E-a1Ir0Q-kjGT5JU7HGdHFs5RWjFi4GIogktPrTFWmA,1829
+kitikiplot/genomics/linear.py,sha256=BNO-9xPVq6dsP8KuXx1fJRG_mLUf2orCM3h7etYqhBw,1280
+kitikiplot-1.0.0.dist-info/LICENSE,sha256=14Bs-3ieyNjj9kCnVLv8CHRXEvQVM6P5uLe-pz7cBI0,1088
+kitikiplot-1.0.0.dist-info/METADATA,sha256=ieqLus54ejy29ZZL6PPjAh-brAch-UxtxmWZy69KtN0,5405
+kitikiplot-1.0.0.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
+kitikiplot-1.0.0.dist-info/RECORD,,

kitikiplot-0.2.8.dist-info/RECORD

@@ -1,12 +0,0 @@
-kitikiplot/core/__init__.py,sha256=7LpJy1V-PZ-JlfjsnRMjMXxTKaFt0JP0mj-A0SgS-sE,34
-kitikiplot/core/kitiki_cell.py,sha256=rWX9DHYMmV1vQEhikWmbgFK5aVnbxZmxSyO0Ra43tn8,8365
-kitikiplot/core/kitiki_color_config.py,sha256=yOWnJNoYo1BN7UMGTFgc8zpMljBbNpFDLLq7JZF3ATE,11857
-kitikiplot/core/kitikiplot.py,sha256=2wCeMipQEEmpnm4uRviwO1JnthdV63B1ic5wFk6gWNI,20835
-kitikiplot/ecology/linear.py,sha256=l1YVn7vcsKU-1g3SZ9kpOhHQiCRqP8U3LrWecy7_KFo,985
-kitikiplot/genomics/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-kitikiplot/genomics/grid.py,sha256=ohg5fBVezzxIOr2TlNPhND4PpBvzVG0eiSklTTbQp5s,1831
-kitikiplot/genomics/linear.py,sha256=BNO-9xPVq6dsP8KuXx1fJRG_mLUf2orCM3h7etYqhBw,1280
-kitikiplot-0.2.8.dist-info/LICENSE,sha256=14Bs-3ieyNjj9kCnVLv8CHRXEvQVM6P5uLe-pz7cBI0,1088
-kitikiplot-0.2.8.dist-info/METADATA,sha256=bHnM3JhlE1LBgc4VdsfNbDLoVNc47QCUGElvTzvIDwU,5445
-kitikiplot-0.2.8.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-kitikiplot-0.2.8.dist-info/RECORD,,