Package: PhyloProfile 1.19.4

Vinh Tran

PhyloProfile: PhyloProfile

PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.

Authors:Vinh Tran [aut, cre], Bastian Greshake Tzovaras [aut], Ingo Ebersberger [aut], Carla Mölbert [ctb]

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PhyloProfile.pdf |PhyloProfile.html✨
PhyloProfile/json (API)
NEWS

# Install 'PhyloProfile' in R:

install.packages('PhyloProfile', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bionf/phyloprofile/issues

Datasets:

filteredProfile - An example of a filtered phylogenetic profile
finalProcessedProfile - An example of a final processed & filtered phylogenetic profile
fullProcessedProfile - An example of a fully processed phylogenetic profile
idList - NCBI ID list for experimental data sets
mainLongRaw - An example of a raw long input file
ppTaxonomyMatrix - An example of a taxonomy matrix
ppTree - An example of a taxonomy tree in newick format
profileWithTaxonomy - An example of a raw long input file together with the taxonomy info
rankList - NCBI rank list for experimental data sets
taxonNamesReduced - NCBI Taxonomy reduced data set
taxonomyMatrix - Taxonomy matrix for experimental data sets

On BioConductor:PhyloProfile-1.19.2(bioc 3.20)PhyloProfile-1.18.0(bioc 3.19)

bioconductor-package

71 exports 1.64 score 125 dependencies 5 mentions

Last updated 15 days agofrom:6413ca542b

Exports:addRankDivisionPlot calcPresSpec checkColorPallete checkInputValidity checkNewick checkOmaID clusterDataDend compareMedianTaxonGroups compareTaxonGroups createArchiPlot createGeneAgePlot createLongMatrix createPercentageDistributionData createProfileFromOma createUnrootedTree createVarDistPlot createVariableDistributionData createVariableDistributionDataSubset dataCustomizedPlot dataFeatureTaxGroup dataMainPlot dataVarDistTaxGroup estimateGeneAge fastaParser featureDistTaxPlot filterProfileData fromInputToProfile geneAgePlotDf generateSinglePlot getAllDomainsOma getAllFastaOma getCommonAncestor getCoreGene getDataClustering getDataForOneOma getDendrogram getDistanceMatrix getFastaFromFasInput getFastaFromFile getFastaFromFolder getIDsRank getInputTaxaID getInputTaxaName getNameList getOmaDataForOneOrtholog getOmaDomainFromURL getOmaMembers getQualColForVector getSelectedFastaOma getSelectedTaxonNames getTaxonomyInfo getTaxonomyMatrix getTaxonomyRanks gridArrangeSharedLegend heatmapPlotting highlightProfilePlot id2name linearizeArchitecture mainTaxonomyRank parseDomainInput parseInfoProfile processNcbiTaxonomy processOrthoID reduceProfile runPhyloProfile sortInputTaxa sortTaxaFromTree taxonomyTableCreator varDistTaxPlot wideToLong xmlParser

Dependencies:AnnotationDbi AnnotationHub ape askpass base64enc Biobase BiocFileCache BiocGenerics BiocManager BiocStyle BiocVersion bioDist Biostrings bit bit64 bitops blob bookdown boot bslib cachem cli colorspace colourpicker commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr digest dplyr DT energy evaluate ExperimentHub extrafont extrafontdb fansi farver fastmap filelock fontawesome fs generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gridExtra gsl gtable highr htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime miniUI munsell nlme openssl pbapply pillar pkgconfig plogr png promises purrr R6 rappdirs RColorBrewer Rcpp RCurl rlang rmarkdown RSQLite Rttf2pt1 S4Vectors sass scales shiny shinyBS shinycssloaders shinyFiles shinyjs sourcetools stringi stringr sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun xml2 xtable XVector yaml zlibbioc zoo

PhyloProfile

Vinh Tran

Rendered fromPhyloProfile-vignette.Rmdusingknitr::rmarkdownon Jun 26 2024.

Last update: 2024-06-03
Started: 2019-03-07

Help page	Topics
Add colors for each feature/domain	addFeatureColors
Add taxonomy rank division lines to the heatmap plot	addRankDivisionPlot
Calculate percentage of present species in each super taxon	calcPresSpec
Check if a color pallete has enough colors for a list of items	checkColorPallete
Check the validity of the input phylogenetic profile file	checkInputValidity
Check the validity of input newick tree	checkNewick
Check the validity of input OMA IDs	checkOmaID
Identify feature type(s) containing overlapped domains/features	checkOverlapDomains
Create a hclust object from the distance matrix	clusterDataDend
Compare the median values of a variable between 2 taxon groups	compareMedianTaxonGroups
Compare the score distributions between 2 taxon groups	compareTaxonGroups
Create protein's domain architecure plot	createArchiPlot
Create gene age plot	createGeneAgePlot
Create a long matrix format for all kinds of input phylogenetic profiles	createLongMatrix
Create data for percentage present taxa distribution	createPercentageDistributionData
Create a phylogenetic profile from a raw OMA dataframe	createProfileFromOma
Create unrooted tree from a taxonomy matrix	createUnrootedTree
Create distribution plot	createVarDistPlot
Create data for additional variable distribution	createVariableDistributionData
Create data for additional variable distribution (for a subset data)	createVariableDistributionDataSubset
Create data for customized profile plot	dataCustomizedPlot
Create data for feature distribution comparison plot	dataFeatureTaxGroup
Create data for main profile plot	dataMainPlot
Create data for variable distribution comparison plot	dataVarDistTaxGroup
Compare the distribution of 2 numeric vectors	distributionTest
Calculate the phylogenetic gene age from the phylogenetic profiles	estimateGeneAge
Parse multi-fasta input file	fastaParser
Create feature distribution comparison plot	featureDistTaxPlot
An example of a filtered phylogenetic profile	filteredProfile
Filter phylogentic profiles	filterProfileData
An example of a final processed & filtered phylogenetic profile	finalProcessedProfile
Complete processing of raw input phylogenetic profiles	fromInputToProfile
An example of a fully processed phylogenetic profile	fullProcessedProfile
Create data for plotting gene ages	geneAgePlotDf
Create a single violin distribution plot	generateSinglePlot
Create domain annotation dataframe from a raw OMA dataframe	getAllDomainsOma
Get all fasta sequences from a raw OMA dataframe	getAllFastaOma
Get all taxa that share a common ancestor	getCommonAncestor
Identify core genes for a list of selected taxa	getCoreGene
Get data for calculating distance matrix from phylogenetic profiles	getDataClustering
Get OMA info for a query protein and its orthologs	getDataForOneOma
Plot dendrogram tree	getDendrogram
Calculate the distance matrix	getDistanceMatrix
Get domain file from a folder for a seed protein	getDomainFolder
Get fasta sequences from main input file in multi-fasta format	getFastaFromFasInput
Get fasta sequences from main input file in multi-fasta format	getFastaFromFile
Get fasta sequences	getFastaFromFolder
Get taxonomy info for a list of taxa	getIDsRank
Get ID list of input taxa from the main input	getInputTaxaID
Get NCBI taxon names for a selected list of taxa	getInputTaxaName
Get list of pre-installed NCBI taxon names	getNameList
Get taxonomy ID, sequence and annotation for one OMA protein	getOmaDataForOneOrtholog
Get domain annotation from OMA Browser	getOmaDomainFromURL
Get OMA members	getOmaMembers
Get color for a list of items	getQualColForVector
Get selected fasta sequences from a raw OMA dataframe	getSelectedFastaOma
Get a subset of input taxa based on a selected taxonomy rank	getSelectedTaxonNames
Get taxonomy hierarchy for a list of taxon IDs	getTaxHierarchy
Get taxonomy info for a list of input taxa	getTaxonomyInfo
Get taxonomy matrix	getTaxonomyMatrix
Create a list containing all main taxanomy ranks	getTaxonomyRanks
Plot Multiple Graphs with Shared Legend in a Grid	gridArrangeSharedLegend
Create profile heatmap plot	heatmapPlotting
Highlight gene and/or taxon of interest on the phylogenetic profile plot	highlightProfilePlot
Get taxon names for a list of taxon IDs	id2name
NCBI ID list for experimental data sets	idList
Join multiple plots and merge legends	joinPlotMergeLegends
Linearize PFAM/SMART annotations by best e-value/bitscore	linearizeArchitecture
An example of a raw long input file	mainLongRaw
Get all NCBI taxonomy rank names	mainTaxonomyRank
Modify feature names	modifyFeatureName
Create architecure plot for a pair of seed and ortholog protein	pairDomainPlotting
Parse domain input file	parseDomainInput
Parsing info for phylogenetic profiles	parseInfoProfile
An example of a taxonomy matrix	ppTaxonomyMatrix
An example of a taxonomy tree in newick format	ppTree
Pre-processing NCBI taxonomy data	processNcbiTaxonomy
Process ortholog IDs	processOrthoID
An example of a raw long input file together with the taxonomy info	profileWithTaxonomy
Create qualitative colours	qualitativeColours
Indexing all available ranks (including norank)	rankIndexing
NCBI rank list for experimental data sets	rankList
Reduce the filtered profile data into supertaxon level	reduceProfile
Modify domain dataframe to resolve overlapped domains/features	resolveOverlapFeatures
Run PhyloProfile app	runPhyloProfile
Create architecure plot for a single protein	singleDomainPlotting
Sort one domain dataframe based on the other domain dataframe	sortDomains
Sort one domain dataframe based on list of ordered feature types	sortDomainsByList
Sort list of (super)taxa based on a selected reference (super)taxon	sortInputTaxa
Get sorted supertaxon list based on a rooted taxonomy tree	sortTaxaFromTree
taxa2dist	taxa2dist
NCBI Taxonomy reduced data set	taxonNamesReduced
Taxonomy matrix for experimental data sets	taxonomyMatrix
Align NCBI taxonomy IDs of list of taxa into a sorted rank list.	taxonomyTableCreator
Create variable distribution comparison plot	varDistTaxPlot
Transform input file in wide matrix into long matrix format	wideToLong
Parse orthoXML input file	xmlParser

Package: PhyloProfile 1.19.4

PhyloProfile: PhyloProfile

PhyloProfile

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