malariagen_data.ag3.Ag3.plot_njt

Ag3.plot_njt(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], n_snps: int, color: str | Mapping | None = None, symbol: str | Mapping | None = None, algorithm: Literal['dynamic', 'rapid', 'canonical'] = 'dynamic', metric: Literal['cityblock', 'euclidean', 'sqeuclidean'] = 'cityblock', distance_sort: bool | None = None, count_sort: bool | None = None, center_x: int | float = 0, center_y: int | float = 0, arc_start: int | float = 0, arc_stop: int | float = 6.283185307179586, width: int | None = 800, height: int | None = 600, show: bool = True, renderer: str | None = None, render_mode: Literal['auto', 'svg', 'webgl'] = 'auto', title: str | bool | None = True, title_font_size: int = 14, line_width: int | float = 0.5, marker_size: int | float = 5, color_discrete_sequence: List | None = None, color_discrete_map: Mapping | None = None, category_orders: List | Mapping | None = None, edge_legend: bool = False, leaf_legend: bool = True, legend_sizing: Literal['constant', 'trace'] = 'constant', thin_offset: int = 0, sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, sample_query_options: dict | None = None, sample_indices: List[int] | None = None, site_mask: str | None = 'default', site_class: str | None = None, min_minor_ac: int | float | None = 2, max_missing_an: int | float | None = 0, cohort_size: int | None = None, min_cohort_size: int | None = None, max_cohort_size: int | None = None, random_seed: int = 42, inline_array: bool = True, chunks: int | str | Tuple[int | str, ...] | Callable[[Tuple[int, ...]], int | str | Tuple[int | str, ...]] = 'native') → Figure | None

Plot an unrooted neighbour-joining tree, computed from pairwise distances between samples using biallelic SNP genotypes.

The tree is displayed as an unrooted tree using the equal angles layout.

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.

n_snpsint

The desired number of SNPs to use when running the analysis. SNPs will be evenly thinned to approximately this number.

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.

algorithm{‘dynamic’, ‘rapid’, ‘canonical’}, optional, default: ‘dynamic’

Neighbour-joining algorithm to use. The ‘dynamic’ algorithm is fastest.

metric{‘cityblock’, ‘euclidean’, ‘sqeuclidean’}, optional, default: ‘cityblock’

The metric to compute distance between genotypes in two samples.

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.

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.

center_xUnionType[int, float], optional, default: 0

X coordinate where plotting is centered.

center_yUnionType[int, float], optional, default: 0

Y coordinate where plotting is centered.

arc_startUnionType[int, float], optional, default: 0

Angle where tree layout begins.

arc_stopUnionType[int, float], optional, default: 6.283185307179586

Angle where tree layout ends.

widthint or None, optional, default: 800

Figure width in pixels (px).

heightint or None, optional, default: 600

Figure 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: ‘auto’

The type of rendering backend to use. See also https://plotly.com/python/webgl-vs-svg/.

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.

line_widthint or float, optional, default: 0.5

Line width.

marker_sizeint or float, optional, default: 5

Marker size.

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.

edge_legendbool, optional, default: False

Show legend entries for the different edge (line) colors.

leaf_legendbool, optional, default: True

Show legend entries for the different leaf node (scatter) colors and symbols.

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.

thin_offsetint, optional, default: 0

Starting index for SNP thinning. Change this to repeat the analysis using a different set of SNPs.

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.

sample_query_optionsdict or None, optional

A dictionary of arguments that will be passed through to pandas query() or eval(), e.g. parser, engine, local_dict, global_dict, resolvers.

sample_indiceslist of int or None, optional

Advanced usage parameter. A list of indices of samples to select, corresponding to the order in which the samples are found within the sample metadata. Either provide this parameter or sample_query, not both.

site_maskstr or None, optional, default: ‘default’

Which site filters mask to apply. See the site_mask_ids property for available values.

site_classstr or None, optional

Select sites belonging to one of the following classes: CDS_DEG_4, (4-fold degenerate coding sites), CDS_DEG_2_SIMPLE (2-fold simple degenerate coding sites), CDS_DEG_0 (non-degenerate coding sites), INTRON_SHORT (introns shorter than 100 bp), INTRON_LONG (introns longer than 200 bp), INTRON_SPLICE_5PRIME (intron within 2 bp of 5’ splice site), INTRON_SPLICE_3PRIME (intron within 2 bp of 3’ splice site), UTR_5PRIME (5’ untranslated region), UTR_3PRIME (3’ untranslated region), INTERGENIC (intergenic, more than 10 kbp from a gene).

min_minor_acint or float or None, optional, default: 2

The minimum minor allele count. SNPs with a minor allele count below this value will be excluded. Can also be a float, which will be interpreted as a fraction.

max_missing_anint or float or None, optional, default: 0

The maximum number of missing allele calls to accept. SNPs with more than this value will be excluded. Set to 0 to require no missing calls. Can also be a float, which will be interpreted as a fraction.

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.

min_cohort_sizeint or None, optional

Minimum cohort size. Raise an error if the number of samples is less than this value.

max_cohort_sizeint or None, optional

Randomly down-sample to this value if the number of samples in the cohort is greater.

random_seedint, optional, default: 42

Random seed used for reproducible down-sampling.

inline_arraybool, optional, default: True

Passed through to dask from_array().

chunksint or str or tuple of int or str or Callable[[typing.Tuple[int, …]], int or str or tuple of int or str], optional, default: ‘native’

Define how input data being read from zarr should be divided into chunks for a dask computation. If ‘native’, use underlying zarr chunks. If a string specifying a target memory size, e.g., ‘300 MiB’, resize chunks in arrays with more than one dimension to match this size. If ‘auto’, let dask decide chunk size. If ‘ndauto’, let dask decide chunk size but only for arrays with more than one dimension. If ‘ndauto0’, as ‘ndauto’ but only vary the first chunk dimension. If ‘ndauto1’, as ‘ndauto’ but only vary the second chunk dimension. If ‘ndauto01’, as ‘ndauto’ but only vary the first and second chunk dimensions. Also, can be a tuple of integers, or a callable which accepts the native chunks as a single argument and returns a valid dask chunks value.

Returns

Figure or None

A plotly figure (only returned if show=False).