SPARCResult

missionbio.demultiplex.phylogeny.state.SPARCResult

class SPARCResult(profile_init: Profile, profile_valid: Profile, profile: Profile, valid_ngts: Dict[str, List[int]], tree_valid: PhyloTree, tree: PhyloTree, labels_valid: Series, labels: Series, events: Dict[str, Any])

A NamedTuple to store the output of predictions by SPARC.

Variables

profile_init	Initial clone genotypes from valid NGT based clustering
profile_valid	Clusters remaining after doublet based assignment
profile	Final clusters present in the phylogeny
valid_ngts	The NGTs allowed for each variant
tree_valid	The initial tree created using ngt_valid
tree	The final phylogenetic tree
labels_valid	The initial labels using ngt_valid
labels	The final labels classifying the cells
events	The events that occurred in each clone in the final tree.

Functions

draw([init])	Draw the phylogenetic tree using plotly
serialize_clones()	Renames the clones as Wildtype, Clone 1, Clone 2, Clone 3...
reorder(barcodes)	Reorder the labels to match the given barcode order.

Create new instance of SPARCResult(profile_init, profile_valid, profile, valid_ngts, tree_valid, tree, labels_valid, labels, events)