CodonU.vizualizer.plot_funcs

Module Contents

Functions

_enc(→ float)

Calculates Theoretical ENC value based on Wright (1989)

_plot_enc(enc_val_lst, gc_val_lst[, organism_name, ...])

Plots ENc value against GC3 values

_plot_pr2(gc_val_lst, at_val_lst, g3_val_lst, a3_val_lst)

Plots A3/AT3 values against G3/GC3 values

_plot_neutrality(gc12_lst, gc3_lst[, organism_name, ...])

Plots the neutrality plot
CodonU.vizualizer.plot_funcs._enc(x: int) → float

Calculates Theoretical ENC value based on Wright (1989)

Parameters:

x – GC3 value

Returns:

ENc value

CodonU.vizualizer.plot_funcs._plot_enc(enc_val_lst: list, gc_val_lst: list, organism_name: None | str = None, save_image: bool = False, folder_path: str = 'Report', gene_analysis: bool = True)

Plots ENc value against GC3 values

Parameters:

  • enc_val_lst – Values of ENc (in range 0 to 1)

  • gc_val_lst – Values of GC3 (in range 0 to 1)

  • organism_name – Name of organism (optional)

  • save_image – Options for saving the image (optional)

  • folder_path – Folder path where image should be saved (optional)

  • gene_analysis – Option if gene analysis (True) or genome analysis (False) (optional)

CodonU.vizualizer.plot_funcs._plot_pr2(gc_val_lst: list, at_val_lst: list, g3_val_lst: list, a3_val_lst: list, organism_name: str | None = None, save_image: bool = False, folder_path: str = 'Report', gene_analysis: bool = True)

Plots A3/AT3 values against G3/GC3 values

Parameters:

  • gc_val_lst – Values of GC3 (in range 0 to 1)

  • at_val_lst – Values of AT3 (in range 0 to 1)

  • g3_val_lst – Values of G3 (in range 0 to 1)

  • a3_val_lst – Values of A3 (in range 0 to 1)

  • organism_name – Name of organism (optional)

  • save_image – Options for saving the image (optional)

  • folder_path – Folder path where image should be saved (optional)

  • gene_analysis – Option if gene analysis (True) or genome analysis (False) (optional)

CodonU.vizualizer.plot_funcs._plot_neutrality(gc12_lst: list, gc3_lst: list, organism_name: None | str = None, save_image: bool = False, folder_path: str = 'Report', gene_analysis: bool = True)

Plots the neutrality plot

Parameters:

  • gc12_lst – The list containing values of G or C at 1 or 2 positions

  • gc3_lst – The list containing values of G or C ar 3 positions

  • organism_name – Name of organism (optional)

  • save_image – Options for saving the image (optional)

  • folder_path – Folder path where image should be saved (optional)

  • gene_analysis – Option if gene analysis (True) or genome analysis (False) (optional)