Dna

class missionbio.mosaic.dna.Dna(*args, **kwargs)

Container for DNA data.

Inherits most methods from missionbio.mosaic.assay._Assay. See that for the documentation on other methods and visualizations.

Algorithms

get_annotations([variants])	Annotate DNA variants.
get_variant_bulk_metrics([variants])	Metrics for each variant.
filter_variants([min_dp, min_gq, vaf_ref, ...])	Find informative variants.
filter_variants_consecutive([proximity])	Remove nearby variants.
filter_barcodes([completeness])	Remove cells with missing information.
find_relevant_variants([...])	Variants that vary across clusters.
find_clones([similarity])	Identify clones based on VAF.
group_by_genotype(features[, layer, ...])	Clusters cells into clones based on the provided variants and returns a dataframe of per-clone and per-variant statistics.
merge_similar_clusters(layer[, similarity])	Merge similar clusters while ignoring missing data.

DNA specific visualizations

plot_variant_correlation()	The correlation of variants across all cells.
update_coloraxis(fig, layer)	Sets the colorscale for DNA.

Extended methods

run_umap(attribute[, output_label, jitter])	Extends _Assay.run_umap()
heatmap(attribute[, splitby, features, ...])	Extends _Assay.heatmap()
feature_scatter(layer, ids, **kwargs)	Extends _Assay.feature_scatter()
scatterplot(attribute[, colorby, features, ...])	Extends _Assay.scatterplot()