singleDomainPlotting {PhyloProfile} | R Documentation

## 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 tran@bio.uni-frankfurt.de

### See Also

`getQualColForVector`, `parseDomainInput`

### Examples

    ## Not run:
    # get domain data
    domainFile <- system.file(
        "extdata", "domainFiles/101621at6656.domains",
        package = "PhyloProfile", mustWork = TRUE
    )
    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
    singleDomainPlotting(
        df,
        geneID,
        sep,
        labelSize, titleSize,
        minStart, maxEnd,
        colorScheme
    )

    ## End(Not run)

[Package PhyloProfile version 1.2.8 Index]