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