# PhyloProfile

## Documentation for package ‘PhyloProfile’ version 1.2.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

calcPresSpec | Calculate percentage of present species in each super taxon
checkInputValidity | Check the validity of the input phylogenetic profile file
checkNewick | Check the validity of input newick tree
checkOmaID | Check the validity of input OMA IDs
clusterDataDend | Create a hclust object from the distance matrix
compareMedianTaxonGroups | Compare the median values of a variable between 2 taxon groups
compareTaxonGroups | Compare the score distributions between 2 taxon groups
createArchiPlot | Create protein's domain architecure plot
createGeneAgePlot | Create gene age plot
createLongMatrix | Create a long matrix format for all kinds of input phylogenetic profiles
createPercentageDistributionData | Create data for percentage present taxa distribution
createProfileFromOma | Create a phylogenetic profile from a raw OMA dataframe
createRootedTree | Create rooted tree from a taxonomy matrix
createVarDistPlot | Create distribution plot
createVariableDistributionData | Create data for additional variable distribution
createVariableDistributionDataSubset | Create data for additional variable distribution (for a subset data)
dataCustomizedPlot | Create data for customized profile plot
dataFeatureTaxGroup | Create data for feature distribution comparison plot
dataMainPlot | Create data for main profile plot
dataVarDistTaxGroup | Create data for variable distribution comparison plot
distributionTest | Compare the distribution of 2 numeric vectors
estimateGeneAge | Calculate the phylogenetic gene age from the phylogenetic profiles
fastaParser | Parse multi-fasta input file
featureDistTaxPlot | Create feature distribution comparison plot
filterProfileData | Filter phylogentic profiles
finalProcessedProfile | An example of a final processed & filtered phylogenetic profile.
fromInputToProfile | Complete processing of raw input phylogenetic profiles
fullProcessedProfile | An example of a fully processed phylogenetic profile.
geneAgePlotDf | Create data for plotting gene ages
generateSinglePlot | Create a single violin distribution plot
getAllDomainsOma | Create domain annotation dataframe from a raw OMA dataframe
getAllFastaOma | Get all fasta sequences from a raw OMA dataframe
getCommonAncestor | Get all taxa that share a common ancestor
getCoreGene | Identify core genes for a list of selected taxa
getDataClustering | Get data for calculating distance matrix from phylogenetic profiles
getDataForOneOma | Get OMA info for a query protein and its orthologs
getDendrogram | Plot dendrogram tree
getDistanceMatrix | Calculate the distance matrix
getDomainFolder | Get domain file from a folder for a seed protein
getFastaFromFasInput | Get fasta sequences from main input file in multi-fasta format
getFastaFromFile | Get fasta sequences from main input file in multi-fasta format
getFastaFromFolder | Get fasta sequences
getIDsRank | Get taxonomy info for a list of taxa
getInputTaxaID | Get ID list of input taxa from the main input
getInputTaxaName | Get NCBI taxon names for a selected list of taxa
getNameList | Get list of pre-installed NCBI taxon names
getOmaDataForOneOrtholog | Get taxonomy ID, sequence and annotation for one OMA protein
getOmaDomainFromURL | Get domain annotation from OMA Browser
getOmaMembers | Get OMA members
getQualColForVector | Get color for a list of items
getSelectedFastaOma | Get selected fasta sequences from a raw OMA dataframe
getSelectedTaxonNames | Get a subset of input taxa based on a selected taxonomy rank
getTaxonomyInfo | Get taxonomy info for a list of input taxa
getTaxonomyMatrix | Get taxonomy matrix
getTaxonomyRanks | Create a list containing all main taxanomy ranks
gridArrangeSharedLegend | Plot Multiple Graphs with Shared Legend in a Grid
heatmapPlotting | Create profile heatmap plot
highlightProfilePlot | Highlight gene and/or taxon of interest on the phylogenetic profile plot
idList | NCBI ID list for experimental data sets
mainLongRaw | An example of a raw long input file.
mainTaxonomyRank | Get all NCBI taxonomy rank names
pairDomainPlotting | Create architecure plot for a pair of seed and ortholog protein
parseDomainInput | Parse domain input file
parseInfoProfile | Parsing info for phylogenetic profiles
ppTaxonomyMatrix | An example of a taxonomy matrix.
ppTree | An example of a taxonomy tree in newick format.
processNcbiTaxonomy | Pre-processing NCBI taxonomy data
profileWithTaxonomy | An example of a raw long input file together with the taxonomy info.
qualitativeColours | Create qualitative colours
rankIndexing | Indexing all available ranks (including norank)
rankList | NCBI rank list for experimental data sets
reduceProfile | Reduce the full processed profile data into supertaxon level
runPhyloProfile | Run PhyloProfile app
singleDomainPlotting | Create architecure plot for a single protein
sortDomains | Sort one domain dataframe based on the other domain dataframe
sortInputTaxa | Sort list of (super)taxa based on a selected reference (super)taxon
sortTaxaFromTree | Get sorted supertaxon list based on a rooted taxonomy tree
taxa2dist | taxa2dist
taxonNamesReduced | NCBI Taxonomy reduced data set
taxonomyMatrix | Taxonomy matrix for experimental data sets
taxonomyTableCreator | Align NCBI taxonomy IDs of list of taxa into a sorted rank list.
varDistTaxPlot | Create variable distribution comparison plot
wideToLong | Transform input file in wide matrix into long matrix format
xmlParser | Parse orthoXML input file