Man pages for BIONF/PhyloProfile
PhyloProfile
| 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 |
| calcPresSpec | Calculate percentage of present species in each super taxon |
| checkColorPalette | Check if a color pallete has enough colors for a list of... |
| 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... |
| clusterDataDend | Create a hclust object from the distance matrix |
| compareMedianTaxonGroups | Compare the median values of a variable between 2 taxon... |
| 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... |
| 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... |
| 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 |
| estimateGeneAge | Calculate the phylogenetic gene age from the phylogenetic... |
| 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... |
| 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... |
| 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... |
| getFastaFromFile | Get fasta sequences from main input file in multi-fasta... |
| 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... |
| heatmapPlotting | Create profile heatmap plot |
| heatmapPlottingFast | Create profile heatmap plot using scattermore |
| highlightProfilePlot | Highlight gene and/or taxon of interest on the phylogenetic... |
| id2name | Get taxon names for a list of taxon IDs |
| idList | NCBI ID list for experimental data sets |
| joinPlotMergeLegends | Join multiple plots and merge legends |
| linearizeArchitecture | Linearize PFAM/SMART annotations by best e-value/bitscore |
| mainLongRaw | An example of a raw long input file |
| mainTaxonomyRank | Get all NCBI taxonomy rank names |
| modifyFeatureName | Modify feature names |
| pairDomainPlotting | Create architecure plot for a pair of seed and ortholog... |
| parseDomainInput | Parse domain input file |
| parseInfoProfile | Parsing info for phylogenetic profiles |
| 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... |
| qualitativeColours | Create qualitative colours |
| 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... |
| runPhyloProfile | Run PhyloProfile app |
| 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... |
| sortInputTaxa | Sort list of (super)taxa based on a selected reference... |
| 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... |
| varDistTaxPlot | Create variable distribution comparison plot |
| wideToLong | Transform input file in wide matrix into long matrix format |
| xmlParser | Parse orthoXML input file |
