rfamSecondaryStructurePlot: Generate a diagram of the secondary structure of an Rfam...
In LaraSellesVidal/rfaRm: An R interface to the Rfam database

Description Usage Arguments Value References Examples

Plots a diagram of the specified type of the secondary structure of an Rfam family. If a filename is provided, the diagram will be saved to the specified path.

1	rfamSecondaryStructurePlot(rfamFamily, filename=NULL, plotType="norm")

`rfamFamily`	string with an Rfam family accession or ID for which the secondary structure should be plotted.
`filename`	string indicating a path to which the plotted diagram should be written. In the default behaviour, filename=NULL, the diagram will not be saved into any file, and instead will only be plotted on R's graphics display. Must be a file type supported by magick, such as PNG, JPEG, GIF, RGB or RGBA.
`plotType`	string indicating the desired type of secondary structure diagram. Can be one of "cons", "fcbp", "cov", "ent", "maxcm", "norm" (default), "rchie", "rscape" or "rscape-cyk". For a description of each type of diagram, see https://docs.rfam.org/en/latest/api.html#secondary-structure-images.

A magick image object with the requested diagram. If a filename was specified, the diagram plot will also be saved to the specified path.

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

# Plot a normal secondary structure diagram of the Rfam family with ID "FMN"

rfamSecondaryStructurePlot("FMN")

# Save a basepair conservation secondary structure diagram of the Rfam family
# with accession "RF00174" as a PNG file.

rfamSecondaryStructurePlot("RF00174", filename="RF00174bpcons.png", plotType="fcbp")