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

In BIONF/PhyloProfile: PhyloProfile

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, showScore, showWeight, namePosition, firstDist,
    nameType, nameSize, segmentSize, nameColor, labelPos, colorPallete, font)

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
showScore	show/hide E-values and Bit-scores. Default = NULL (hide)
showWeight	Show/hide feature weights. Default = NULL (hide)
namePosition	list of positions for domain names, choose from "plot", "legend" or "axis". Default: "plot"
firstDist	distance of the first domain to plot title. Default = 0.5
nameType	type of domain names, either "Texts" or "Labels" (default)
nameSize	Size of domain names. Default = 3
segmentSize	Height of domain segment. Default = 5
nameColor	color of domain names (for Texts only). Default = "black"
labelPos	position of domain names (for Labels only). Choose from "Above" (default), "Below" or "Inside" the domain bar
colorPallete	color pallete. Default = Paired"
font	font of text. Default = Arial"

Value

Domain plot of a pair proteins as a arrangeGrob object.

Author(s)

Vinh Tran [e-mail]

See Also

singleDomainPlotting, sortDomains, parseDomainInput

Examples

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")
domainDf$feature_id_mod <- domainDf$feature_id
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))
# resolve overlapping domains
seedDf <- PhyloProfile:::resolveOverlapFeatures(seedDf)
orthoDf <- PhyloProfile:::resolveOverlapFeatures(orthoDf)
# add feature colors
featureColorDf <- PhyloProfile:::addFeatureColors(seedDf, orthoDf)
seedDf <- featureColorDf[[1]]
orthoDf <- featureColorDf[[2]]
# do plot
g <- PhyloProfile:::pairDomainPlotting(
   seed,ortho,seedDf,orthoDf,minStart,maxEnd, font = "sans"
)
grid::grid.draw(g)

BIONF/PhyloProfile documentation built on Aug. 3, 2024, 11:53 a.m.