Man pages for BIONF/PhyloProfile
PhyloProfile

calcPresSpecCalculate percentage of present species in each super taxon
checkInputValidityCheck the validity of the input phylogenetic profile file
checkNewickCheck the validity of input newick tree
checkOmaIDCheck the validity of input OMA IDs
clusterDataDendCreate a hclust object from the distance matrix
compareMedianTaxonGroupsCompare the median values of a variable between 2 taxon...
compareTaxonGroupsCompare the score distributions between 2 taxon groups
createArchiPlotCreate protein's domain architecure plot
createGeneAgePlotCreate gene age plot
createLongMatrixCreate a long matrix format for all kinds of input...
createPercentageDistributionDataCreate data for percentage present taxa distribution
createProfileFromOmaCreate a phylogenetic profile from a raw OMA dataframe
createRootedTreeCreate rooted tree from a taxonomy matrix
createVarDistPlotCreate distribution plot
createVariableDistributionDataCreate data for additional variable distribution
createVariableDistributionDataSubsetCreate data for additional variable distribution (for a...
dataCustomizedPlotCreate data for customized profile plot
dataFeatureTaxGroupCreate data for feature distribution comparison plot
dataMainPlotCreate data for main profile plot
dataVarDistTaxGroupCreate data for variable distribution comparison plot
distributionTestCompare the distribution of 2 numeric vectors
estimateGeneAgeCalculate the phylogenetic gene age from the phylogenetic...
fastaParserParse multi-fasta input file
featureDistTaxPlotCreate feature distribution comparison plot
filterProfileDataFilter phylogentic profiles
finalProcessedProfileAn example of a final processed & filtered phylogenetic...
fromInputToProfileComplete processing of raw input phylogenetic profiles
fullProcessedProfileAn example of a fully processed phylogenetic profile.
geneAgePlotDfCreate data for plotting gene ages
generateSinglePlotCreate a single violin distribution plot
getAllDomainsOmaCreate domain annotation dataframe from a raw OMA dataframe
getAllFastaOmaGet all fasta sequences from a raw OMA dataframe
getCommonAncestorGet all taxa that share a common ancestor
getCoreGeneIdentify core genes for a list of selected taxa
getDataClusteringGet data for calculating distance matrix from phylogenetic...
getDataForOneOmaGet OMA info for a query protein and its orthologs
getDendrogramPlot dendrogram tree
getDistanceMatrixCalculate the distance matrix
getDomainFolderGet domain file from a folder for a seed protein
getFastaFromFasInputGet fasta sequences from main input file in multi-fasta...
getFastaFromFileGet fasta sequences from main input file in multi-fasta...
getFastaFromFolderGet fasta sequences
getIDsRankGet taxonomy info for a list of taxa
getInputTaxaIDGet ID list of input taxa from the main input
getInputTaxaNameGet NCBI taxon names for a selected list of taxa
getNameListGet list of pre-installed NCBI taxon names
getOmaDataForOneOrthologGet taxonomy ID, sequence and annotation for one OMA protein
getOmaDomainFromURLGet domain annotation from OMA Browser
getOmaMembersGet OMA members
getQualColForVectorGet color for a list of items
getSelectedFastaOmaGet selected fasta sequences from a raw OMA dataframe
getSelectedTaxonNamesGet a subset of input taxa based on a selected taxonomy rank
getTaxonomyInfoGet taxonomy info for a list of input taxa
getTaxonomyMatrixGet taxonomy matrix
getTaxonomyRanksCreate a list containing all main taxanomy ranks
gridArrangeSharedLegendPlot Multiple Graphs with Shared Legend in a Grid
heatmapPlottingCreate profile heatmap plot
highlightProfilePlotHighlight gene and/or taxon of interest on the phylogenetic...
idListNCBI ID list for experimental data sets
mainLongRawAn example of a raw long input file.
mainTaxonomyRankGet all NCBI taxonomy rank names
pairDomainPlottingCreate architecure plot for a pair of seed and ortholog...
parseDomainInputParse domain input file
parseInfoProfileParsing info for phylogenetic profiles
ppTaxonomyMatrixAn example of a taxonomy matrix.
ppTreeAn example of a taxonomy tree in newick format.
processNcbiTaxonomyPre-processing NCBI taxonomy data
profileWithTaxonomyAn example of a raw long input file together with the...
qualitativeColoursCreate qualitative colours
rankIndexingIndexing all available ranks (including norank)
rankListNCBI rank list for experimental data sets
reduceProfileReduce the full processed profile data into supertaxon level
runPhyloProfileRun PhyloProfile app
singleDomainPlottingCreate architecure plot for a single protein
sortDomainsSort one domain dataframe based on the other domain dataframe
sortInputTaxaSort list of (super)taxa based on a selected reference...
sortTaxaFromTreeGet sorted supertaxon list based on a rooted taxonomy tree
taxa2disttaxa2dist
taxonNamesReducedNCBI Taxonomy reduced data set
taxonomyMatrixTaxonomy matrix for experimental data sets
taxonomyTableCreatorAlign NCBI taxonomy IDs of list of taxa into a sorted rank...
varDistTaxPlotCreate variable distribution comparison plot
wideToLongTransform input file in wide matrix into long matrix format
xmlParserParse orthoXML input file
BIONF/PhyloProfile documentation built on July 21, 2020, 5:27 p.m.