singleDomainPlotting: Create architecure plot for a single protein

In BIONF/PhyloProfile: PhyloProfile

Create architecure plot for a single protein

Description

Create architecure plot for a single protein

Usage

singleDomainPlotting(df, geneID, sep, labelSize, titleSize, minStart,
    maxEnd, colorPalette, showScore, showWeight, namePosition, firstDist,
    nameType, nameSize, segmentSize, nameColor, labelPos, font)

Arguments

df	Domain dataframe for ploting containing the seed ID, ortholog ID, ortholog 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)
geneID	ID of seed or orthologous protein
sep	Separate indicator for title. Default = "|"
labelSize	Lable size. Default = 12
titleSize	Title size. Default = 12
minStart	The smallest start position of all domains
maxEnd	The highest stop position of all domains
colorPalette	Color pallete. Default = Paired"
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
font	font of text. Default = Arial"

Value

Domain plot of a single protein as a ggplot object.

Author(s)

Vinh Tran [e-mail]

See Also

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:::singleDomainPlotting(
   seedDf, seed, minStart = minStart, maxEnd = maxEnd, font = "sans"
)
grid::grid.draw(g)

BIONF/PhyloProfile documentation built on Sept. 25, 2024, 4:46 p.m.