Plot protein sequence(s)

plotProteinSeq draws the sequences of proteins within the same "ProteinSeq" object. In this format, more similar sequences will have similar banding patterns.

Usage

plotProteinSeq(x, taxon.to.plot, knitr = FALSE)

Arguments

x

A "ProteinSeq" object containing proteins from taxon1 and taxon2.

taxon.to.plot

A character vector providing the common name of the species that will be plotted. Must be a name present in x.

knitr

Logical indicating if plot is intended to show up in RMarkdown files made by the Knitr R package.

Value

A draw of the protein sequence(s) provided. Colors refer to specific amino acids ("R", "W", "I", "F", "S", "T", "N", "H", "K", "D", "G", "L", "Y", "V", "M", "A", "E", "P", "Q", "C")", "gaps/space in the sequence ("-"), ambiguous amino acid ("B" - often representing either asparagine ("N") or aspartic acid ("D")), or another marker for ambiguous amino acid ("X").

See also

Other macroevolution: calcFossilDivTT(), checkAndFixUltrametric(), countSeqDiffs(), estimateSpeciation(), fitCRBD(), lttPlot(), plotPaintedWhales(), plotRawFossilOccs(), simulateBirthDeathRich(), simulateTree()

Author

Matheus Januario, Jennifer Auler

Examples

data(cytOxidase)
plotProteinSeq(cytOxidase, c("human", "chimpanzee", "cnidaria"), knitr = TRUE)