Dna#
missionbio.mosaic.dna.Dna
- class Dna(*args, **kwargs)#
Container for DNA data.
Inherits most methods from
_Assay. See that for the documentation on other methods and visualizations.Algorithms#
get_annotations([variants, genome])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.
mutated_cells(labels[, variants, kind, layer])The count/fraction of cells that are mutated for each clone.
DNA specific visualizations#
The correlation of variants across all cells.
update_coloraxis(fig, layer[, coloraxis])Sets the colorscale for DNA.
Extended methods#
run_umap(attribute[, output_label, jitter])Extends
run_umap()heatmap(attribute[, splitby, features, ...])Extends
heatmap()feature_scatter(layer, ids, **kwargs)Extends
feature_scatter()scatterplot(attribute[, colorby, features, ...])Extends
scatterplot()