ANI.graph: Construct an undirected graph using pairwise ANI values

In lmc297/bactaxR: Bacterial taxonomy construction and evaluation in R

Construct an undirected graph using pairwise ANI values

Description

This function constructs an undirected graph using pairwise ANI values calculated between genomes and the similarity metric described by Carroll, Wiedmann, and Kovac (2019).

Usage

ANI.graph(
  bactaxRObject,
  ANI_threshold = 95,
  graphopt_charge = 0.02,
  graphout_niter = 500,
  edge_color = hcl(h = 168, c = 5, l = 58, alpha = 0.1),
  metadata = NULL,
  color_palette = plasma(n = length(unique(metadata))),
  node_size = 3,
  show_legend = T,
  legend_pos_x = -2,
  legend_pos_y = 1,
  legend_cex = 0.5,
  legend_ncol = 1
)

Arguments

bactaxRObject	A bactaxRObject
ANI_threshold	ANI threshold; an edge will be drawn between two genomes whose pairwise ANI value is greater than or equal to this threshold. Defaults to 95.
graphopt_charge	Charge parameter passed to layout_with_graphopt function in the igraph package. Defaults to 0.02.
graphout_niter	Number of iterations to perform for layout_with_graphopt funtion in the igraph package. Defaults to 500.
edge_color	Color of edges in graph. Defaults to gray, specifically hcl(h = 168, c = 5, l = 58, alpha = 0.1).
metadata	Named vector, where names correspond to node names, and vector elements correspond to metadata to map to nodes (e.g., species name). Vector names must match node names exactly. Defaults to NULL (no metadata stupplied).
color_palette	Vector of colors to apply to nodes. Defaults to one color (using the plasma color scale) per unique metadata value, i.e., plasma(n = length(unique(metadata))).
node_size	Size of nodes in graph. Defaults to 3.
show_legend	Display legend (True or False). Defaults to True.
legend_pos_x	x coordinate used to position the legend. Default is -2.
legend_pos_y	y coordinate used to position the legend. Default is 1.
legend_cex	Character expansion factor relative to current “‘par("cex")“' to pass to R’s “'legend“' function. Defaults to 0.5.
legend_ncol	Number of columns to display in legend. Defaults to 1.

Value

A plot object

lmc297/bactaxR documentation built on Feb. 6, 2024, 7:41 p.m.