rfamSeedTreeImage: Get an image of the phylogenetic tree of the seed multiple...

In rfaRm: An R interface to the Rfam database

Description

Plots an image of the phylogenetic tree of the seed multiple alignment associated to the Rfam family. If a filename is provided, the image will be saved to the path specified through filename. The tree can be labeled with species names or sequence accessions.

Usage

rfamSeedTreeImage(rfamFamily, filename=NULL, label="species")

Arguments

rfamFamily	string with an Rfam family accession or ID for which the phylogenetic tree of the seed alignment should be plotted.
filename	string indicating a path to which the plot of the phylogenetic tree should be written.
label	string indicating the type of labels that should be added to the plot of the phylogenetic tree. Should be either "species" for labeling with species names (default) or "acc" for labeling with sequence accessions.

Value

A magick image object with the requested phylogenetic tree plot in GIF format. If a filename was specified, the phylogenetic tree plot will also be saved to the specified path.

References

Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P Nawrocki, Elena Rivas, Sean R Eddy, Alex Bateman, Robert D Finn, Anton I Petrov, Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D335–D342, https://doi.org/10.1093/nar/gkx1038

https://docs.rfam.org/en/latest/api.html

Examples

# Display a plot of the phylogenetic tree of the seed alignment for the Rfam
# family with ID "FMN" labeled with species names

rfamSeedTreeImage("FMN", label="species")

# Display a plot of the phylogenetic tree of the seed alignment for the Rfam
# family with accession "RF00147" labeled with sequence accessions and save it
# to a PNG file.

rfamSeedTreeImage("RF00147", filename="RF00147seedTreeImage.png", label="acc")

rfaRm documentation built on March 16, 2021, 6:01 p.m.