API¶

Command Line Interface¶

Plot variants from the given VCF file.

param in_vcf: path of the input VCF file
param linear: plot variants on a linear plot rather than a polar one [default: False]
param sample: specific sample to plot (defaults to all available samples)
param save: if true, the final plot will be saved to a file [default: False]
param output: path of the output file where the plot will be saved
param labels: if true, add a label for each variant shown [default: False]
param labels_hf: if true and labels=True, show HF value in each variant’s label [default: False]
param legend: if true, add a legend for loci colors in the plot [default: False]
param split: if true, plot split H and L strands [default: False]
param interactive: if true, create an interactive version of the plot [default: False]

Plot variant from the given pandas DataFrame.

param in_df: input pandas DataFrame
param linear: plot variants on a linear plot rather than a polar one [default: False]
param sample: specific sample to plot (defaults to all available samples)
param save: if true, the final plot will be saved to a file [default: False]
param output: path of the output file where the plot will be saved
param labels: if true, add a label for each variant shown [default: False]
param labels_hf: if true and labels=True, show HF value in each variant’s label [default: False]
param legend: if true, add a legend for loci colors in the plot [default: False]
param split: if true, plot split H and L strands [default: False]
param interactive: if true, create an interactive version of the plot [default: False]
param pos_col: column name for the variant position
param ref_col: column name for the variant reference allele
param alt_col: column name for the variant alternate allele
param sample_col: column name for the variant sample
param hf_col: column name for the variant heteroplasmic fraction

Plot variants from the given tabular file.

param in_table: path of the input tabular file
param sep: column delimiter used [default: ‘,’]
param linear: plot variants on a linear plot rather than a polar one [default: False]
param sample: specific sample to plot (defaults to all available samples)
param save: if true, the final plot will be saved to a file [default: False]
param output: path of the output file where the plot will be saved
param labels: if true, add a label for each variant shown [default: False]
param labels_hf: if true and labels=True, show HF value in each variant’s label [default: False]
param legend: if true, add a legend for loci colors in the plot [default: False]
param split: if true, plot split H and L strands [default: False]
param interactive: if true, create an interactive version of the plot [default: False]
param pos_col: column name for the variant position
param ref_col: column name for the variant reference allele
param alt_col: column name for the variant alternate allele
param sample_col: column name for the variant sample
param hf_col: column name for the variant heteroplasmic fraction
param **kwargs: additional arguments passed to pandas.read_table()