Package index • hospitraceRVisualize

Phylogeny and trace plots

Plot phylogenetic trees alongside per-patient location traces, the headline figures of the package.

plot_trace_phylo_tree(): Plot a phylogeny with a location trace heatmap
plot_trace_phylo_legend(): Create a standalone legend for trace phylogeny plots
plot_trace_phylo_presence(): Plot a phylogeny with a presence/absence trace heatmap and surveillance overlay
plot_clusters_phylo(): Map clusters onto a phylogenetic tree

Cluster comparison and overlap plots

Visualize comparisons between cluster assignments and epidemiological overlap analyses.

plot_jaccard_similarity_heatmap(): Plot a heatmap of Jaccard similarity between two clusterings
plot_overlap_perm_test(): Plot overlap permutation test results as violin plots

Cluster statistics plots

Summarize genetic variation within and between transmission clusters.

plot_genetic_distance_by_cluster(): Plot the per-isolate genetic distance needed to cluster each isolate, by cluster
plot_intra_vs_inter_cluster_distance(): Plot max intra-cluster vs. min inter-cluster genetic distance
plot_intra_vs_inter_isolate_distance(): Plot max intra-cluster vs. min inter-isolate genetic distance