seqinr: plot.SeqAcnucWeb – R documentation

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plot.SeqAcnucWeb

To Plot Subsequences on the Parent Sequence

Description

This function plots all the type of subsequences on a parent sequence. Subsequences are represented by colored rectangle on the parent sequence. For example, types could be CDS, TRNA, RRNA .... In order to get all the types that are available for the selected database, use getType.

Usage

## S3 method for class 'SeqAcnucWeb'
plot(x, types = getType()$sname, socket = autosocket(), ...)

Arguments

`x`	A sequence of class `SeqAcnucWeb`
`types`	The type of subsequences to plot. Default value is to consider all possible subsequence types.
`socket`	an object of class `sockconn` connecting to a remote ACNUC database (default is a socket to the last opened database).
`...`	not currently used

Value

An invisible list giving, for each subsequence, its position on the parent sequence.

Author(s)

D. Charif, J.R. Lobry

References

http://doua.prabi.fr/databases/acnuc.html

citation("seqinr")

Examples

## Not run:  
  ### Need internet connection
  choosebank("emblTP")
  mylist <- query("mylist", "AC=AB078009")	
  plot(mylist$req[[1]])
  
## End(Not run)

seqinr

Biological Sequences Retrieval and Analysis

v4.2-16

GPL (>= 2)

Authors

Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]

Initial release

2022-05-19