PhyloProfile

Documentation for package ‘PhyloProfile’ version 1.19.12

Help Pages

-- A --

addFeatureColors	Add colors for each feature/domain
addRankDivisionPlot	Add taxonomy rank division lines to the heatmap plot
addUmapTaxaColors	Add colors for taxa in UMAP 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
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
createUmapPlotData	Create UMAP cluster plot
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
distributionTest	Compare the distribution of 2 numeric vectors

-- E --

estimateGeneAge

Calculate the phylogenetic gene age from the phylogenetic profiles

-- F --

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
groupLabelUmapData	Reduce the number of labels for UMAP 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
plotUmap	Create UMAP cluster plot
ppTaxonomyMatrix	An example of a taxonomy matrix
ppTree	An example of a taxonomy tree in newick format
prepareUmapData	Prepare data for UMAP
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.

-- U --

umapClustering

Perform UMAP clustering

-- 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