searchtree: Function to grep search labels in tree and plot all connected...

In celiason/phenotools: Tools for the analysis and assembly of phenomic data in R

Function to grep search labels in tree and plot all connected components

Description

Function to grep search labels in tree and plot all connected components

Usage

searchtree(graph, pattern, plot = TRUE, mode = "out", ...)

Arguments

graph	(required) input graph of trait ontology generated by, e.g., read_ontology() or stemsearch()
pattern	text to search for (regular expression)
plot	whether to plot (logical)
mode	whether to search for all edges to current node ("in") or away from ("out")
...	additional arguments passed to the 'plot.igraph' function

References

Baumel, J. J., and L. M. Witmer. 1993. Osteologia. P. in Handbook of avian anatomy: nomina anatomica avium. Publications of the Nuttall Ornithological Club.

Examples

## Not run: 
# load Baumel and Whitmer (1993) ontology:
ont <- read_ontology(file = system.file("extdata", "baumel_ontology.txt",
package = "phenotools"))
# show all traits in ontology under "orbita"
searchtree(ont, "\\borbita\\b")

## End(Not run)

celiason/phenotools documentation built on Sept. 29, 2024, 5:43 p.m.