seqinr: draw.recstat – R documentation

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draw.recstat

Graphical representation of a recstat analysis.

Description

This function displays the results returned by recstat with two plots. The first one shows the factor scores of a CA computed on the codon composition of a DNA sequence. The second one shows the locations of all Start and Stop codons in this sequence.

Usage

draw.recstat(rec, fac = 1, direct  = TRUE, xlim = c(1, seqsize),
    col = c("red", "blue", "purple"))

Arguments

`rec`	list of elements returned by `recstat` function.
`fac`	axis of the CA to use for display (4 ≥ `fac` ≥ 1).
`direct`	a logical for the choice of direct or reverse strand.
`xlim`	starting and ending positions in the sequence for the plot.
`col`	vector of colour codes for the three frames of the sequence.

Details

The first plot shows the factor scores of the sliding windows, this for the three possible frames of the strand selected by the user. The second shows the Start (filled grey triangles pointing up) and Stop (solid black triangles pointing down) codons positions. Note that the standard genetic code is used for that purpose. Visual detection of putative CDS is performed through the simultaneous use of these two graphics. If a CDS is located within the sequence, the factor scores for the windows located in the corresponding reading frame will be significantly separated from the two others. Moreover, the region where this separation is seen should be located between a Start and a Stop codon.

Author(s)

O. Clerc, G. Perrière

Examples

ff <- system.file("sequences/ECOUNC.fsa", package = "seqinr")
seq <- read.fasta(ff)
rec <- recstat(seq[[1]], seqname = getName(seq))
draw.recstat(rec)

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