visualize_chromosome_region

pylluminator.visualizations.visualize_chromosome_region(samples: Samples, chromosome_id: int | str, start_pos: int, end_pos: int, apply_mask: bool = True, keep_na: bool = False, protein_coding_only=False, custom_sheet: DataFrame | None = None, figsize: tuple[float, float] = (15, 10), save_path: None | str = None, var: None | str | list[str] = None, gene_name: str | None = None, padding=0, row_factors: str | list[str] | None = None, row_legends: str | list[str] | None = '') → None

Show the beta values of a gene for all probes and samples in its transcription zone.

Parameters:

  • samples (Samples) – samples with beta values already calculated

  • apply_mask (bool) – True removes masked probes from betas, False keeps them. Default: True

  • keep_na (bool) – set to True to only output probes with no NA value for any sample. Default: False

  • protein_coding_only (bool) – limit displayed transcripts to protein coding ones. Default: False

  • custom_sheet (pandas.DataFrame) – a sample sheet to use. By default, use the samples’ sheet. Useful if you want to filter the samples to display

  • var (None | str | list[str]) – a column name or list of column names from the samplesheet to add to the heatmap labels. Default: None

  • figsize (tuple[float, float]) – size of the whole plot. Default: (15, 15)

  • save_path (str | None) – if set, save the graph to save_path. Default: None

  • row_factors (str | list[str] | None) – list of columns to show as color categories on the side of the heatmap. Must correspond to columns of the sample sheet. Default: None

  • row_legends (str | list[str] | None) – list of columns to generate a legend for. Set to None for no legends. Only work for columns also specified in row_factors. Default: ‘’ (generate all legends)

  • padding – length in kb pairs to add at the end and beginning of the transcription zone. Default: 0

  • gene_name (str | None) – name of the gene, if applicable, to output in the title. Default: None

Type:

int

Returns:

None