pairDomainPlotting {PhyloProfile} | R Documentation

## Create architecure plot for a pair of seed and ortholog protein

### 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 tran@bio.uni-frankfurt.de

### 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)

[Package PhyloProfile version 1.4.11 Index]