taxa_edgelist: Get Edgelist from Tax Table

In krisrs1128/treelapse: Visualization for Tree-Structured Collections of Counts and Series

Description

This is a helper to construct edgelists using tax tables. This is useful when we want to visualize the tree associated with a taxonomy (which can have more than two children, unlike the phylos that usually come with a phyloseq object).

Usage

taxa_edgelist(taxa)

Arguments

taxa

[matrix] A matrix (with rownames) whose first column represents the highest level in the hierarchy, next level is next depth, etc, and whose rownames represent the finest level name (e.g., OTU in the phyloseq context). NAs can be used to represent that finer level information is not available; in this case, the tree skips these levels in the tree.

Value

el [data.frame] A two column data.frame (parent & child) giving a list of edges associated with the taxonomic tree.

Examples

taxa <- matrix(
  c("1", "2", "1", NA, "1", NA, "1", "6"),
    nrow = 4,
    byrow = TRUE,
    dimnames = list(c("3", "4", "5", "7"),
                    c("depth_1", "depth_2"))
   )
taxa_edgelist(taxa)

krisrs1128/treelapse documentation built on Jan. 3, 2020, 6:29 p.m.