trviz.visualizer

Module Contents

Classes

TandemRepeatVisualizer

class trviz.visualizer.TandemRepeatVisualizer
static encode_tr_sequence(labeled_motifs)
static _get_unique_labels(aligned_repeats)
static plot_motif_color_map(symbol_to_motif, motif_counter, symbol_to_color, file_name, figure_size=None, box_size=1, box_margin=0.1, label_size=None, dpi=300)

Generate a plot for motif color map

trplot(aligned_labeled_repeats: List[str], sample_ids: List[str], figure_size: Tuple[int, int] = None, output_name: str = None, dpi: int = 300, alpha: float = 0.6, box_line_width: float = 0, hide_xticks: bool = False, hide_yticks: bool = False, symbol_to_motif: Dict[str, str] = None, sort_by_clustering: bool = True, hide_dendrogram: bool = True, population_data: str = None, motif_marks: Dict[str, str] = None, allele_as_row: bool = True, xlabel_size: int = 8, ylabel_size: int = 8, xlabel_rotation: int = 0, ylabel_rotation: int = 0, private_motif_color: str = 'black', frame_on: Dict[str, bool] = None, debug: bool = False)

Generate a plot showing the variations in tandem repeat sequences. A distinct color is assigned to each motif. For private motifs (with low frequency), the same color (in black by default) may be assigned.

Parameters

  • aligned_labeled_repeats – aligned and encoded tandem repeat sequences.

  • sample_ids – sample IDs

  • figure_size – figure size

  • output_name – output file name

  • dpi – DPI for the plot

  • alpha – alpha value for the plot

  • box_line_width – line width for box edges

  • hide_xticks – if true, hide xticks

  • hide_yticks – if true, hide yticks

  • symbol_to_motif – a dictionary mapping symbols to motifs

  • sort_by_clustering – if true, sort the samples by clustering

  • hide_dendrogram – if true, hide the dendrogram

  • population_data – population data file name

  • motif_marks – a dictionary mapping sample to motif marks

  • allele_as_row – if true, plot allele as row (default is true)

  • xlabel_size – x label size (default is 8)

  • ylabel_size – y label size (default is 8)

  • xlabel_rotation – x label rotation (default is 0)

  • ylabel_rotation – y label rotation (default is 0)

  • private_motif_color – the color for private motifs. Default is black

  • frame_on – a dictionary mapping sample to frame on. Default is {‘top’: False, ‘bottom’: True, ‘right’: False, ‘left’: True}

  • debug – if true, print verbose information.

add_dendrogram(fig, aligned_labeled_repeats, sample_ids, symbol_to_motif, hide_clustering)

Add dendrogram to the figure.

figmatplotlib.figure.Figure

Figure to add dendrogram to.

aligned_labeled_repeatslist of list of str

List of aligned labeled repeats.

sample_idslist of str

List of sample ids.

symbol_to_motifdict of str to str

Dictionary mapping symbols to motifs.

hide_clusteringbool

Whether to hide clustering.

sorted_sample_idslist of str

List of sorted sample ids.

sorted_aligned_labeled_repeatslist of list of str

List of sorted aligned labeled repeats.

static get_symbol_to_color_map(alpha, unique_symbol_count, unique_symbols)
set_symbol_to_color_map(symbol_to_color)
get_population_colormap(population_data)

Allowed super populations: {AMR, AFR, EAS, SAS, EUR}