createArchiPlot: Create protein's domain architecure plot

In PhyloProfile: PhyloProfile

Description

Create architecture plot for both seed and orthologous protein. If domains of ortholog are missing, only architecture of seed protein will be plotted. NOTE: seed protein ID is the one being shown in the profile plot, which normally is also the orthologous group ID.

Usage

createArchiPlot(info = NULL, domainDf = NULL, labelArchiSize = 12,
    titleArchiSize = 12)

Arguments

info	a list contains seed and ortholog's IDs
domainDf	dataframe contains domain info for the seed and ortholog. This including the seed ID, orthologs IDs, sequence lengths, feature names, start and end positions, feature weights (optional) and the status to determine if that feature is important for comparison the architecture between 2 proteins* (e.g. seed protein vs ortholog) (optional).
labelArchiSize	lable size (in px). Default = 12.
titleArchiSize	title size (in px). Default = 12.

Value

A domain plot as arrangeGrob object. Use grid::grid.draw(plot) to render.

Author(s)

Vinh Tran [e-mail]

See Also

singleDomainPlotting, sortDomains, parseDomainInput, getQualColForVector

Examples

seedID <- "101621at6656"
orthoID <- "101621at6656|AGRPL@224129@0|224129_0:001955|1"
info <- c(seedID, orthoID)
domainFile <- system.file(
    "extdata", "domainFiles/101621at6656.domains",
    package = "PhyloProfile", mustWork = TRUE
)
domainDf <- parseDomainInput(seedID, domainFile, "file")
plot <- createArchiPlot(info, domainDf, 9, 9)
grid::grid.draw(plot)

Example output

Warning message:
In RColorBrewer::brewer.pal(n = n, name = "Set1") :
  minimal value for n is 3, returning requested palette with 3 different levels

PhyloProfile documentation built on March 27, 2021, 6:01 p.m.