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 = "GeneID", sep = "|", labelSize = 12,
    titleSize = 12, minStart = NULL, maxEnd = NULL, colorScheme)

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
colorScheme	color scheme for all domain types

Value

Domain plot of a single protein as a ggplot object.

Author(s)

Vinh Tran [e-mail]

See Also

getQualColForVector, parseDomainInput

Examples

## Not run: 
# get domain data
domainFile <- system.file(
    "extdata", "domainFiles/101621at6656.domains",
    package = "PhyloProfile", mustWork = TRUE
)
seedID <- "101621at6656"
domainDf <- parseDomainInput(seedID, domainFile, "file")
df <- domainDf[
    domainDf$orthoID == "101621at6656:AGRPL@224129@0:224129_0:001955:1",]
# create color scheme for all domain types
allFeatures <- levels(as.factor(df$feature))
allColors <- getQualColForVector(allFeatures)
colorScheme <- structure(
    allColors,
    .Names = allFeatures
)
# other parameters
geneID <- "AGRPL@224129@0|224129_0:001955|1"
sep <- "|"
labelSize <- 9
titleSize <- 9
minStart <- min(df$start)
maxEnd <- max(df$end)
# do plotting
PhyloProfile:::singleDomainPlotting(
    df,
    geneID,
    sep,
    labelSize, titleSize,
    minStart, maxEnd,
    colorScheme
)

## End(Not run)

BIONF/PhyloProfile documentation built on April 14, 2024, 10:39 p.m.