CodonU.vizualizer

Submodules

Package Contents

Functions

plot_enc(handle, genetic_table_num[, ...])

Plots ENc curve from given fasta file

plot_pr2

plot_neutrality

plot_phy_dnd(handle[, title, save_image, folder_path])

Plots phylogenetic tree from dnd file

plot_phy_nex

plot_phy_fas(handle[, title, save_image, folder_path])

Plots phylogenetic tree from fasta file

plot_ca_codon_freq_codon(handle, genetic_table_num[, ...])

Plots CA of codon frequency for codons with frequency as scale

plot_ca_codon_freq_gene(handle, genetic_table_num[, ...])

Plots CA for genes with gene length as scale

plot_ca_codon_rscu_codon(handle, genetic_table_num[, ...])

Plots CA of codon RSCU for codons with frequency as scale

plot_ca_codon_rscu_gene(handle, genetic_table_num[, ...])

Plots CA of codon RSCU for genes with frequency as scale

plot_ca_aa_freq_aa

plot_ca_aa_freq_gene(handle, genetic_table_num, scale)

Plots CA for genes with aromaticity or gravy score as scale.
CodonU.vizualizer.plot_enc(handle: str | Any, genetic_table_num: int, min_len_threshold: int = 200, organism_name: None | str = None, save_image: bool = False, folder_path: str = 'Report', gene_analysis: bool = True)

Plots ENc curve from given fasta file

Parameters:

  • handle – Handle to the file, or the filename as a string

  • genetic_table_num – Genetic table number for codon table

  • min_len_threshold – Minimum length of nucleotide sequence to be considered as gene

  • 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_pr2(handle: str | Any, min_len_threshold: int = 200, organism_name: str | None = None, save_image: bool = False, folder_path: str = '', gene_analysis: bool = True)

Plots A3/AT3 values against G3/GC3 values from given fasta file

Parameters:

  • handle – Handle to the file, or the filename as a string

  • min_len_threshold – Minimum length of nucleotide sequence to be considered as gene

  • 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_neutrality(handle: str | Any, min_len_threshold: int = 200, organism_name: str | None = None, save_image: bool = False, folder_path: str = '', gene_analysis: bool = True)

Plots neutrality plot from given fasta file

Parameters:

  • handle – Handle to the file, or the filename as a string

  • min_len_threshold – Minimum length of nucleotide sequence to be considered as gene

  • 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_phy_dnd(handle: str, title: str = 'Phylogenetic Tree', save_image: bool = False, folder_path: str = 'Report')

Plots phylogenetic tree from dnd file

Parameters:

  • handle – Handle to the dnd file

  • title – Title of the plot

  • save_image – Options for saving the image (optional)

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

CodonU.vizualizer.plot_phy_nex(handle: str, title: str = 'Phylogenetic Tree', save_image: bool = False, folder_path: str = 'Report')

Plots phylogenetic tree from nexus file

Parameters:

  • handle – Handle to the nexus file

  • title – Title of the plot

  • save_image – Options for saving the image (optional)

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

CodonU.vizualizer.plot_phy_fas(handle: str, title: str = 'Phylogenetic Tree', save_image: bool = False, folder_path: str = 'Report')

Plots phylogenetic tree from fasta file

Parameters:

  • handle – Handle to the fasta file

  • title – Title of the plot

  • save_image – Options for saving the image (optional)

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

CodonU.vizualizer.plot_ca_codon_freq_codon(handle: str, genetic_table_num: int, min_len_threshold: int = 200, n_components: int = 2, single_syn_codons: list | None = None, organism_name: str | None = None, save_image: bool = False, folder_path: str = 'Report')

Plots CA of codon frequency for codons with frequency as scale

Parameters:

  • handle – Handle to the file, or the filename as a string

  • genetic_table_num – Genetic table number for codon table

  • min_len_threshold – Minimum length of nucleotide sequence to be considered as gene (optional)

  • n_components – Components for CA (Optional)

  • single_syn_codons – List of codons belonging to SF1 (optional)

  • organism_name – Name of organism (optional)

  • save_image – Options for saving the image (optional)

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

CodonU.vizualizer.plot_ca_codon_freq_gene(handle: str, genetic_table_num: int, min_len_threshold: int = 200, n_components: int = 2, single_syn_codons: list | None = None, organism_name: str | None = None, save_image: bool = False, folder_path: str = 'Report')

Plots CA for genes with gene length as scale

Parameters:

  • handle – Handle to the file, or the filename as a string

  • genetic_table_num – Genetic table number for codon table

  • min_len_threshold – Minimum length of nucleotide sequence to be considered as gene (optional)

  • n_components – Components for CA (Optional)

  • single_syn_codons – List of codons belonging to SF1 (optional)

  • organism_name – Name of organism (optional)

  • save_image – Options for saving the image (optional)

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

CodonU.vizualizer.plot_ca_codon_rscu_codon(handle: str, genetic_table_num: int, min_len_threshold: int = 200, n_components: int = 2, single_syn_codons: list | None = None, organism_name: str | None = None, save_image: bool = False, folder_path: str = 'Report')

Plots CA of codon RSCU for codons with frequency as scale

Parameters:

  • handle – Handle to the file, or the filename as a string

  • genetic_table_num – Genetic table number for codon table

  • min_len_threshold – Minimum length of nucleotide sequence to be considered as gene (optional)

  • n_components – Components for CA (Optional)

  • single_syn_codons – List of codons belonging to SF1 (optional)

  • organism_name – Name of organism (optional)

  • save_image – Options for saving the image (optional)

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

CodonU.vizualizer.plot_ca_codon_rscu_gene(handle: str, genetic_table_num: int, min_len_threshold: int = 200, n_components: int = 2, single_syn_codons: list | None = None, organism_name: str | None = None, save_image: bool = False, folder_path: str = 'Report')

Plots CA of codon RSCU for genes with frequency as scale

Parameters:

  • handle – Handle to the file, or the filename as a string

  • genetic_table_num – Genetic table number for codon table

  • min_len_threshold – Minimum length of nucleotide sequence to be considered as gene (optional)

  • n_components – Components for CA (Optional)

  • single_syn_codons – List of codons belonging to SF1 (optional)

  • organism_name – Name of organism (optional)

  • save_image – Options for saving the image (optional)

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

CodonU.vizualizer.plot_ca_aa_freq_aa(handle: str, genetic_table_num: int, min_len_threshold: int = 66, n_components: int = 2, organism_name: str | None = None, save_image: bool = False, folder_path: str = 'Report')

Plots CA of aa frequency for genes with frequency as scale.

Parameters:

  • handle – Handle to the file, or the filename as a string

  • genetic_table_num – Genetic table number for codon table

  • min_len_threshold – Minimum length of nucleotide sequence to be considered as gene (optional)

  • n_components – Components for CA (Optional)

  • organism_name – Name of organism (optional)

  • save_image – Options for saving the image (optional)

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

CodonU.vizualizer.plot_ca_aa_freq_gene(handle: str, genetic_table_num: int, scale: str, min_len_threshold: int = 66, n_components: int = 2, organism_name: str | None = None, save_image: bool = False, folder_path: str = 'Report')

Plots CA for genes with aromaticity or gravy score as scale.

NOTE Values of scale supported are ‘gravy’, ‘aroma’

Parameters:

  • handle – Handle to the file, or the filename as a string

  • genetic_table_num – Genetic table number for codon table

  • scale – Scale for gene colors

  • min_len_threshold – Minimum length of nucleotide sequence to be considered as gene (optional)

  • n_components – Components for CA (Optional)

  • organism_name – Name of organism (optional)

  • save_image – Options for saving the image (optional)

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