malariagen_data.ag3.Ag3.plot_haplotype_clustering#
- Ag3.plot_haplotype_clustering(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], analysis: str = 'default', sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, cohort_size: int | None = None, random_seed: int = 42, color: str | Mapping | None = None, symbol: str | Mapping | None = None, linkage_method: Literal['single', 'complete', 'average', 'weighted', 'centroid', 'median', 'ward'] = 'single', count_sort: bool | None = None, distance_sort: bool | None = None, title: str | bool | None = True, title_font_size: int = 14, width: int | None = None, height: int | None = 500, show: bool = True, renderer: str | None = None, render_mode: Literal['auto', 'svg', 'webgl'] = 'svg', leaf_y: int = 0, marker_size: int | float = 5, line_width: int | float = 0.5, line_color: str = 'black', color_discrete_sequence: List | None = None, color_discrete_map: Mapping | None = None, category_orders: List | Mapping | None = None, legend_sizing: Literal['constant', 'trace'] = 'constant') Figure | None #
Hierarchically cluster haplotypes in region and produce an interactive plot.
Parameters#
- regionstr or Region or Mapping or list of str or Region or Mapping or tuple of str or Region or Mapping
Region of the reference genome. Can be a contig name, region string (formatted like “{contig}:{start}-{end}”), or identifier of a genome feature such as a gene or transcript. Can also be a sequence (e.g., list) of regions.
- analysisstr, optional, default: ‘default’
Which haplotype phasing analysis to use. See the phasing_analysis_ids property for available values.
- sample_setssequence of str or str or None, optional
List of sample sets and/or releases. Can also be a single sample set or release.
- sample_querystr or None, optional
A pandas query string to be evaluated against the sample metadata, to select samples to be included in the returned data.
- cohort_sizeint or None, optional
Randomly down-sample to this value if the number of samples in the cohort is greater. Raise an error if the number of samples is less than this value.
- random_seedint, optional, default: 42
Random seed used for reproducible down-sampling.
- colorstr or Mapping or None, optional
Name of variable to use to color the markers.
- symbolstr or Mapping or None, optional
Name of the variable to use to choose marker symbols.
- linkage_method{‘single’, ‘complete’, ‘average’, ‘weighted’, ‘centroid’, ‘median’, ‘ward’}, optional, default: ‘single’
The linkage algorithm to use. See the Linkage Methods section of the scipy.cluster.hierarchy.linkage docs for full descriptions.
- count_sortbool or None, optional
If True, for each node n, the child with the minimum number of descendants is plotted first. Note distance_sort and count_sort cannot both be True.
- distance_sortbool or None, optional
If True, for each node n, if True, the child with the minimum distance between is plotted first. Note distance_sort and count_sort cannot both be True.
- titlestr or bool or None, optional, default: True
If True, attempt to use metadata from input dataset as a plot title. Otherwise, use supplied value as a title.
- title_font_sizeint, optional, default: 14
Font size for the plot title.
- widthint or None, optional
Plot width in pixels (px).
- heightint or None, optional, default: 500
Plot height in pixels (px).
- showbool, optional, default: True
If true, show the plot. If False, do not show the plot, but return the figure.
- rendererstr or None, optional
The name of the renderer to use.
- render_mode{‘auto’, ‘svg’, ‘webgl’}, optional, default: ‘svg’
The type of rendering backend to use. See also https://plotly.com/python/webgl-vs-svg/.
- leaf_yint, optional, default: 0
Y coordinate at which to plot the leaf markers.
- marker_sizeint or float, optional, default: 5
Marker size.
- line_widthint or float, optional, default: 0.5
Line width.
- line_colorstr, optional, default: ‘black’
Line color.
- color_discrete_sequenceList or None, optional
Provide a list of colours to use.
- color_discrete_mapMapping or None, optional
Provide an explicit mapping from values to colours.
- category_ordersList or Mapping or None, optional
Control the order in which values appear in the legend.
- legend_sizing{‘constant’, ‘trace’}, optional, default: ‘constant’
Determines if the legend items symbols scale with their corresponding “trace” attributes or remain “constant” independent of the symbol size on the graph.
Returns#
- Figure or None
A plotly figure (only returned if show=False).