Changes in version 1.20.4 o added t-SNE dimension reduction o highlight genes and taxa for sub-plot o use fastcluster for clustering and sorting the input taxa Changes in version 1.20.3 o fixed bug with NCBI taxonomy link at the first time running o improve UMAP 3D (hover info, dot zooming, same colors with 2D plot) Changes in version 1.20.2 o hover option for UMAP o UMAP 3D using plotly o fixed bug with Point's info Changes in version 1.20.1 o auto identify refspec o fixed subsetting data using a list of gene IDs Changes in version 1.20.0 o added UMAP clustering o improved domain plot #110 o fast mode for large profile plot o option to change font o option to show gene names o option to sort genes by defined list o option to upload preprocessed data from an input folder Changes in version 1.18.0 o option to specify version for OrthoDB Changes in version 1.16.5 o fixed detailed plot when name of a taxon is substring of another o show supertaxon names when rotate the profile plot Changes in version 1.16.3 o fixed clustering method not applied Changes in version 1.16.2 o check if taxonomy DB exists in cwd instead of r/library Changes in version 1.16.1 o fixed bug wrong order in detailed plot o fixed bug mVar for co-orthologs Changes in version 1.16.0 o extended options in config file o option to specify IP and port o able to generate domain plot from main/customized profile tab o highlight multiple genes/taxa; division lines for taxon group (#110) o simplify gene IDs in detailed plot; show taxonomy hierarchy (#110) o option to filter features in architecture plot (#110) o option to show all input taxa (#110) o added more info to domain plot (e-value, bit-score, pHMM) o option to specify host and port for runPhyloProfile() fn o fixed bug when lowest rank is subspecies Changes in version 1.14.5 o improved highlighted duplicated ortho IDs Changes in version 1.14.4 o fixed bug ordering genes o auto identify lowest rank Changes in version 1.14.2 o option to use user defined taxonomy DB (#124) Changes in version 1.14.1 o option for highlight duplicated ortholog IDs o option for cluster profiles based on ortholog IDs o speedup by pre-calculating taxonomy tree (#123) o disable rank selection after plotting o turn on profile clustering by default o changed "ftp://" to "https://" for taxdmp.zip o fixed #126 Changes in version 1.14.0 o option for uploading sorted taxon list Changes in version 1.12.6 o fixed bug ordering gene IDs when using gene categories Changes in version 1.12.5 o fixed bug multiple entries for one (super)taxon ID Changes in version 1.12.4 o fixed bug download data Changes in version 1.12.3 o fixed bug customized profile not showed Changes in version 1.12.1 o added number of co-orthologs and number of taxa in each supertaxon o replaced pfam link by interpro url Changes in version 1.10.3 o fixed bug parsing taxon names for input with more than 9999 taxa Changes in version 1.10.1 o fixed bug button for tree uploading disappear #119 o improved parsing seq ID to create links for external DB #117 o fixed bug grepping domains for group comparison fn o fixed bug parsing data for a list of input gene IDs #122 Changes in version 1.8.6 o option to identify sequence source Changes in version 1.8.5 o added functions for exporting plot settings Changes in version 1.8.4 o fixed error reading taxonNamesReduced.txt that contains "#" o added functions for import and export taxonomy DB Changes in version 1.8.3 o fixed bug of group comparison function Changes in version 1.8.2 o fixed loading cluster from config file Changes in version 1.8.1 o do not show pfam links for smart domains and vice versa Changes in version 1.7.8 o only mainInput is required in config file Changes in version 1.7.7 o use config file for input files, refspec selection and othes settings Changes in version 1.6.6 o turn off auto sizing for large number of taxa or genes (>= 10.000) Changes in version 1.6.5 o fixed filter for "species relation" o added midpoint colors Changes in version 1.6.2 o increase default font size for profile and domain plot o make links to DBs: ncbi taxonomy, ncbi protein, uniprot, pfam, smart Changes in version 1.6.1 o modified taxonomy ranks (ropensci#875) o improved rank indexing function (ropensci#874) o improved x-axis label (#116) Changes in version 1.4.12 o domain plot works with group ID containing pipe Changes in version 1.4.11 o added check for invalid ids in newTaxa file Changes in version 1.4.10 o fixed bug comparing unk taxon IDs with max ncbi taxID Changes in version 1.4.9 o fixed bug comparing taxon IDs with max ncbi taxID Changes in version 1.4.8 o fixed bug filterProfileData (some filtered data could not be plotted) Changes in version 1.4.5 o Add auto sizing feature Changes in version 1.4.4 o Fixed orthoxml parsing function Changes in version 1.4.3 o Plot background for NA orthologs o Fixed highlight by categories Changes in version 1.4.2 o Fixed error when parsing large amount of new taxa o Improved the speed of parsing new taxa o Apply filter to refspec orthologs when not working with strain/species Changes in version 1.4.1 o Fixed bug data lost after filtering var2 o Add filter data to detailed plot Changes in version 1.3.11 o Add filter number of co-orthologs to parseInfoProfile() Changes in version 1.3.10 o Calculate percentage of present taxa after filtering of var1 and var2 o Fixed filter when working with high taxonomy ranks Changes in version 1.2.8 o Added new NCBI taxonomy ranks (e.g. biotype, isolate, pathogroup, ...) o Added function to reset taxonomy data Changes in version 1.2.7 o Solved problem with new NCBI taxonomy rank "clade" by replace them with "norank" Changes in version 1.2.6 o Fixed bug customized profile of subset of taxa not clickable Changes in version 1.2.4 o Fixed bug checking invalid taxon IDs Changes in version 1.2.1 o Fixed bug in rankIndexing and processNcbiTaxonomy o Improved check for invalid input taxon IDs Changes in version 1.1.12 o Added pseudo IDs for Holozoa and Holomycota clades and their non-NCBI sub-clades Changes in version 1.1.11 o Increased the resolution of the phylostratigraphy function Changes in version 1.1.10 o Improved the rank indexing function Changes in version 1.1.6 o Removed grDevices, grid, stats, utils from Imports list in DESCRIPTION Changes in version 1.1.5 o Added progress indicators for data loading and processing steps o Removed shinycssloaders Changes in version 1.1.3 o Fixed bug listing taxa by selecting a supertaxon from a higher level o Added message for downloading preprocessed data Changes in version 1.1.2 o Fixed bug sorting taxa when taxonomy rank is set as strain Changes in version 1.1.1 o Commented examples of OMA parser functions o Turned off tests for OMA parser functions Changes in version 0.99.31 o Submitted to Bioconductor