# PhyloProfile

## Documentation for package ‘PhyloProfile’ version 2.4.1

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

## Help Pages

A C D E F G H I J L M P Q R S T V W X

## -- A --

addDimRedTaxaColors | Add colors for taxa in dimension reduction plot
addFeatureColors | Add colors for each feature/domain
addRankDivisionPlot | Add taxonomy rank division lines to the heatmap plot

## -- C --

calcPresSpec | Calculate percentage of present species in each super taxon
checkColorPalette | Check if a color pallete has enough colors for a list of items
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
checkOverlapDomains | Identify feature type(s) containing overlapped domains/features
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
createDimRedPlotData | Generate data for dimension reduction 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
createUnrootedTree | Create unrooted 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)

## -- D --

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
dimReduction | Perform dimension reduction 2D
distributionTest | Compare the distribution of 2 numeric vectors

## -- E --

estimateGeneAge | Calculate the phylogenetic gene age from the phylogenetic profiles

## -- F --

fallbackUmap | Fallback for UMAP in case of insufficient samples
fastaParser | Parse multi-fasta input file
featureDistTaxPlot | Create feature distribution comparison plot
filteredProfile | An example of a filtered phylogenetic profile
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

## -- G --

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
getTaxHierarchy | Get taxonomy hierarchy for a list of taxon IDs
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
groupLabelDimRedData | Reduce the number of labels for DIM reduction plot based on the gene/taxon frequency

## -- H --

heatmapPlotting | Create profile heatmap plot
heatmapPlottingFast | Create profile heatmap plot using scattermore
highlightProfilePlot | Highlight gene and/or taxon of interest on the phylogenetic profile plot

## -- I --

id2name | Get taxon names for a list of taxon IDs
idList | NCBI ID list for experimental data sets

## -- J --

joinPlotMergeLegends | Join multiple plots and merge legends

## -- L --

linearizeArchitecture | Linearize PFAM/SMART annotations by best e-value/bitscore

## -- M --

mainLongRaw | An example of a raw long input file
mainTaxonomyRank | Get all NCBI taxonomy rank names
modifyFeatureName | Modify feature names

## -- P --

pairDomainPlotting | Create architecure plot for a pair of seed and ortholog protein
parseDomainInput | Parse domain input file
parseInfoProfile | Parsing info for phylogenetic profiles
performPCA | Helper function to perform PCA
performUmap | Helper function to handle UMAP logic
plotDimRed | Create dimension reduction plot
plotDimRed3D | Create dimension reduction 3D plot
ppTaxonomyMatrix | An example of a taxonomy matrix
ppTree | An example of a taxonomy tree in newick format
prepareDimRedData | Prepare data for dimension reduction
processNcbiTaxonomy | Pre-processing NCBI taxonomy data
processOrthoID | Process ortholog IDs
profileWithTaxonomy | An example of a raw long input file together with the taxonomy info

## -- Q --

qualitativeColours | Create qualitative colours

## -- R --

rankIndexing | Indexing all available ranks (including norank)
rankList | NCBI rank list for experimental data sets
reduceProfile | Reduce the filtered profile data into supertaxon level
resolveOverlapFeatures | Modify domain dataframe to resolve overlapped domains/features
runPhyloProfile | Run PhyloProfile app

## -- S --

singleDomainPlotting | Create architecure plot for a single protein
sortDomains | Sort one domain dataframe based on the other domain dataframe
sortDomainsByList | Sort one domain dataframe based on list of ordered feature types
sortInputTaxa | Sort list of (super)taxa based on a selected reference (super)taxon
sortTaxaFromTree | Get sorted supertaxon list based on a rooted taxonomy tree

## -- T --

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.

## -- V --

varDistTaxPlot | Create variable distribution comparison plot

## -- W --

wideToLong | Transform input file in wide matrix into long matrix format

## -- X --

xmlParser | Parse orthoXML input file