ANI.dendrogram: Construct a dendrogram using pairwise ANI values and identity...
| ANI.dendrogram | R Documentation |
Construct a dendrogram using pairwise ANI values and identity medoid genomes
Description
This function constructs a dendrogram using pairwise ANI values calculated between genomes and the dissimilarity metric described by Carroll, Wiedmann, and Kovac (2019), yielding medoid genomes and cluster assignments at an ANI coalescence threshold (if supplied by the user).
Usage
ANI.dendrogram(
bactaxRObject,
ANI_threshold = 95,
hclust.method = "average",
label_size = 1e-10,
color_palette = magma(1000, begin = 0.2),
xline = NULL,
xlinecol = "#20A387FF",
xlinetype = "dashed"
)
Arguments
bactaxRObject |
A bactaxRObject |
ANI_threshold |
ANI threshold at which to assign genomes to clusters and identify medoid genomes. Defaults to 95. |
hclust.method |
Agglomeration method to pass to hclust. Defaults to "average". |
label_size |
Size of dendrogram tip labels. Defaults to an arbitrarily small number (i.e., 1e-10), so that tip labels are hidden. |
color_palette |
Color palette to use for dendrogram. Defaults to magma(1000, begin = 0.2). |
xline |
Numeric value (or vector of numeric values) at which to draw vertical line(s) along the dendrogram X-axis (i.e., ANI values). Defaults to NULL (no vertical lines). |
xlinecol |
Character (or vector of characters) corresponding to ggplot2 color(s) for xline. Defaults to "#20A387FF". |
xlinetype |
Character (or vector of characters) corresponding to ggplot2 line type(s) for xline. Defaults to "dashed". |
Value
medoid_genomes A data frame of medoid genomes detected at an ANI threshold (ANI_threshold). If an ANI threshold of NULL supplied, this will be NULL.
cluster_assignments A data frame containing all genomes and the genomospecies clusters to which they are assigned at an ANI threshold (ANI_threshold). If an ANI threshold of NULL is supplied, this will be NULL.
