dataCustomizedPlot {PhyloProfile} | R Documentation

## Create data for customized profile plot

### Description

Create data for customized profile plot based on a selected list of genes and/or taxa, containing seed protein IDs (geneID), ortholog IDs (orthoID) together with their ncbi taxonomy IDs (ncbiID and abbrName), full names (fullName), indexed supertaxa (supertaxon), values for additional variables (var1, var2) and the aggregated values of those additional variables for each supertaxon (mVar1, mVar2), number of original and filtered co-orthologs in each supertaxon (paralog and paralogNew), number of species in each supertaxon (numberSpec) and the each supertaxon (presSpec).

### Usage

    dataCustomizedPlot(dataHeat = NULL, selectedTaxa = "all",
        selectedSeq = "all")

### Arguments

`dataHeat` | a data frame contains processed profiles (see ?fullProcessedProfile, ?filterProfileData)
`selectedTaxa` | selected subset of taxa. Default = "all".
`selectedSeq` | selected subset of genes. Default = "all".

### Value

A dataframe contains data for plotting the customized profile.

### Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

### See Also

`filterProfileData`

### Examples

    data("superTaxonProfile", package="PhyloProfile")
    selectedTaxa <- c("Mammalia", "Saccharomycetes", "Insecta")
    selectedSeq <- "all"
    dataCustomizedPlot(superTaxonProfile, selectedTaxa, selectedSeq)

[Package PhyloProfile version 1.4.11 Index]