pairDomainPlotting: Create architecure plot for a pair of seed and ortholog...

In PhyloProfile: PhyloProfile

Description

Create architecure plot for a pair of seed and ortholog protein

Usage

pairDomainPlotting(seed, ortho, seedDf, orthoDf, minStart, maxEnd, 
    labelSize, titleSize)

Arguments

seed	Seed ID
ortho	Ortho ID
seedDf	domain dataframe for seed domains containing the seed ID, ortholog ID, sequence length, 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).
orthoDf	domain dataframe for ortholog domains (same format as seedDf).
minStart	the smallest start position of all domains
maxEnd	the highest stop position of all domains
labelSize	lable size. Default = 12.
titleSize	title size. Default = 12.

Value

Domain plot of a pair proteins as a arrangeGrob object.

Author(s)

Vinh Tran [e-mail]

Examples

## Not run: 
seed <- "101621at6656"
ortho <- "101621at6656|AGRPL@224129@0|224129_0:001955|1"
ortho <- gsub("\\|", ":", ortho)
grepID <- paste(seed, "#", ortho, sep = "")
domainFile <- system.file(
    "extdata", "domainFiles/101621at6656.domains",
    package = "PhyloProfile", mustWork = TRUE
)
domainDf <- parseDomainInput(seed, domainFile, "file")
subdomainDf <- domainDf[grep(grepID, domainDf$seedID), ]
subdomainDf$feature <- as.character(subdomainDf$feature)
orthoDf <- subdomainDf[subdomainDf$orthoID == ortho,]
seedDf <- subdomainDf[subdomainDf$orthoID != ortho,]
minStart <- min(subdomainDf$start)
maxEnd <- max(c(subdomainDf$end, subdomainDf$length))
g <- pairDomainPlotting(seed,ortho,seedDf,orthoDf,minStart,maxEnd,9,9)    
grid::grid.draw(g)

## End(Not run)

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