Package index • mitodrift

Core workflow

MitoDrift: MitoDrift R6 Class

Clades and support

add_clade_freq(): Add clade frequencies to a phylogenetic tree
collect_chains(): Collect MCMC chains into a multiPhylo object

trim_tree(): Collapse weak clades below a confidence threshold.
assign_clones_polytomy(): Assign clone IDs to a tree allowing small polytomies.

Diagnostics

compute_variant_pr_curve(): Compute variant-to-tree precision/recall/F1 curve across confidence cutoffs
plot_prec_recall_vs_conf(): Plot precision/recall/F1 versus confidence cutoff

Visualization

plot_phylo_circ(): Plot Circular Phylogenetic Tree with Annotations
plot_phylo_heatmap2(): Plot a phylogenetic tree with VAF heatmap and annotations
make_clade_pal(): Build a named Brewer palette with optional cycling behavior

Data utilities

mat_to_long(): Convert allele count matrix (amat) and total count matrix (dmat) to long format
long_to_mat(): Convert a long format mutation data frame to a matrix
phylo_to_gtree(): Convert a phylo object to a tbl_graph
add_node_names(): Add "Node" labels to the internal nodes of a phylo tree

Example data

pL1000_tree_annot: Annotated phylogenetic tree for pL1000_200_1
pL1000_mut_dat: Mutation count data for pL1000_200_1