createArchiPlot: Create protein's domain architecure plot
In BIONF/PhyloProfile: PhyloProfile

createArchiPlot

R Documentation

Create protein's domain architecure plot

Description

Create architecture plot for both seed and orthologous protein. If domains of ortholog are missing, only architecture of seed protein will be plotted. NOTE: seed protein ID is the one being shown in the profile plot, which normally is also the orthologous group ID.

Usage

createArchiPlot(info, domainDf, labelArchiSize, titleArchiSize,
    showScore, showWeight, namePosition, firstDist, nameType, nameSize,
    segmentSize, nameColor, labelPos, colorType, ignoreInstanceNo,
    currentNCBIinfo, featureClassSort, featureClassOrder, colorPalette,
    resolveOverlap, font)

Arguments

`info`	A list contains seed and ortholog's IDs
`domainDf`	Dataframe contains domain info for the seed and ortholog. This including the seed ID, orthologs IDs, sequence lengths, 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).
`labelArchiSize`	Lable size (in px). Default = 12.
`titleArchiSize`	Title size (in px). 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
`colorType`	Choose to color "all", "shared", "unique" features or color by "Feature type". Default = "all"
`ignoreInstanceNo`	Ignore number of feature instances while identifying shared or unique features. Default = FALSE
`currentNCBIinfo`	Dataframe of the pre-processed NCBI taxonomy data. Default = NULL (will be automatically retrieved from PhyloProfile app)
`featureClassSort`	Choose to sort features. Default = "Yes"
`featureClassOrder`	vector of ordered feature classes
`colorPalette`	Choose between "Paired", "Set1", "Set2", "Set3", "Accent", "Dark2" for the color pallete
`resolveOverlap`	Choose to merge non-overlapped features of a feature type into one line. Default = "Yes"
`font`	font of text. Default = Arial"

Value

A domain plot as arrangeGrob object. Use grid::grid.draw(plot) to render.

Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

Examples

seedID <- "101621at6656"
orthoID <- "101621at6656|AGRPL@224129@0|224129_0:001955|1"
info <- c(seedID, orthoID)
domainFile <- system.file(
    "extdata", "domainFiles/101621at6656.domains",
    package = "PhyloProfile", mustWork = TRUE
)
domainDf <- parseDomainInput(seedID, domainFile, "file")
domainDf$feature_id_mod <- domainDf$feature_id
domainDf$feature_id_mod <- gsub("SINGLE", "LCR", domainDf$feature_id_mod)
domainDf$feature_id_mod[domainDf$feature_type == "coils"] <- "Coils"
domainDf$feature_id_mod[domainDf$feature_type == "seg"] <- "LCR"
domainDf$feature_id_mod[domainDf$feature_type == "tmhmm"] <- "TM"
plot <- createArchiPlot(info, domainDf, font = "sans")
grid::grid.draw(plot)

BIONF/PhyloProfile documentation built on Oct. 12, 2024, 3:37 p.m.