API¶
Command Line Interface¶
Python Module¶
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()