addFeatureColors: Add colors for each feature/domain

In BIONF/PhyloProfile: PhyloProfile

Add colors for each feature/domain

Description

Add colors to features/domains of 2 domain dataframes. Users can choose to color only the shared features, unique features, all features (default) or based on feature types. Default color pallete is "Paired", but it can be changed.

Usage

addFeatureColors(
  seedDf = NULL,
  orthoDf = NULL,
  colorType = "all",
  colorPalette = "Paired",
  ignoreInstanceNo = FALSE
)

Arguments

seedDf	Domain dataframe of seed protein (protein 1)
orthoDf	Domain dataframe of orthologs protein (protein 2)
colorType	Choose to color "all", "shared", "unique" features or color by "Feature type". Default: "all"
colorPalette	Choose between "Paired", "Set1", "Set2", "Set3", "Accent", "Dark2" for the color pallete
ignoreInstanceNo	Ignore number of feature instances while identifying shared or unique features. Default: FALSE

Value

2 dataframes (seedDf and orthoDf) with an additional column for the assigned color to each feature instance

Author(s)

Vinh Tran [e-mail]

Examples

# get domain data
seedID <- "101621at6656"
domainFile <- system.file(
    "extdata", "domainFiles/101621at6656.domains",
    package = "PhyloProfile", mustWork = TRUE
)
domainDf <- parseDomainInput(seedID, domainFile, "file")
# get seedDf and orthoDf
subDf <- domainDf[
    domainDf$seedID ==
    "101621at6656#101621at6656:AGRPL@224129@0:224129_0:001955:1",]
orthoDf <- subDf[subDf$orthoID == "101621at6656:DROME@7227@1:Q9VG04",]
seedDf <- subDf[subDf$orthoID != "101621at6656:DROME@7227@1:Q9VG04",]
# add colors to features
PhyloProfile:::addFeatureColors(seedDf, orthoDf)

BIONF/PhyloProfile documentation built on Dec. 18, 2024, 7:33 a.m.