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

Description Usage Arguments Value Author(s) Examples

View source: R/createDomainPlot.R

Description

Create architecure plot for a pair of seed and ortholog protein

Usage

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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 tran@bio.uni-frankfurt.de

Examples

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## 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.