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NEWS
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CHANGES IN VERSION 1.51.1
-----------------------
o Update email address.
CHANGES IN VERSION 1.49.1
-----------------------
o Fix the issue for importMatrix when 'w' is missing.
CHANGES IN VERSION 1.47.1
-----------------------
o Update documentation of motifStack function.
CHANGES IN VERSION 1.45.1
-----------------------
o Fix the issue of 'This picture was not generated by Cairo graphics' for importSVG.
CHANGES IN VERSION 1.41.1
-----------------------
o Fix the issue of importMatrix for mixed cases of alphabet in MEME format.
CHANGES IN VERSION 1.39.4
-----------------------
o Change the fontfamily from 'mono,Courier' to 'mono' in vignettes.
CHANGES IN VERSION 1.39.3
-----------------------
o add XMatrix format for importMatrix.
CHANGES IN VERSION 1.39.2
-----------------------
o Accept scales for y-axis for logo when ic.scale is FALSE.
CHANGES IN VERSION 1.39.1
-----------------------
o Accept user defined x-axis for logo.
CHANGES IN VERSION 1.37.5
-----------------------
o Change the style of motifPile.
CHANGES IN VERSION 1.37.5
-----------------------
o Fix the bug of the ylab grid.
CHANGES IN VERSION 1.37.4
-----------------------
o Fix the bug that the rownames were not checked for alignment.
CHANGES IN VERSION 1.37.3
-----------------------
o Fix the bug method argument of matAlign is ignored.
CHANGES IN VERSION 1.37.2
-----------------------
o Improve importMatrix to read the tags from file.
CHANGES IN VERSION 1.37.1
-----------------------
o handle the error "failed to load cairo DLL"
CHANGES IN VERSION 1.35.2
-----------------------
o Add rmarkdown as suggest package.
CHANGES IN VERSION 1.33.14
-----------------------
o remove reverse complement alignment for RNA motifs.
CHANGES IN VERSION 1.33.13
-----------------------
o narrow the predefined font.
CHANGES IN VERSION 1.33.12
-----------------------
o fix the issue for pcm2pfm if the column counts are not identical.
CHANGES IN VERSION 1.33.11
-----------------------
o update the markers to allow label + line/rect.
CHANGES IN VERSION 1.33.10
-----------------------
o add alignment function for AA motifs.
CHANGES IN VERSION 1.33.9
-----------------------
o fix the issue for AA motif of clusterMotifs
CHANGES IN VERSION 1.33.8
-----------------------
o fix the issue of symbol position for predefined font
CHANGES IN VERSION 1.33.7
-----------------------
o update check ghostscript
CHANGES IN VERSION 1.33.6
-----------------------
o fix the bug in pcm2pssm
CHANGES IN VERSION 1.33.5
-----------------------
o fix the bug in pcm2pssm
CHANGES IN VERSION 1.33.4
-----------------------
o add pssm class
CHANGES IN VERSION 1.33.3
-----------------------
o replace MotIV by matalign.
o add cutoffPval for motifSignature function.
CHANGES IN VERSION 1.33.2
-----------------------
o add parameter environment for coloredSymbols
CHANGES IN VERSION 1.33.1
-----------------------
o change grImport, grImport2 and MotIV to Suggests.
o use roxygen2 to generate help files.
CHANGES IN VERSION 1.31.2
-----------------------
o reduce the compiling time for vignettes.
CHANGES IN VERSION 1.31.1
-----------------------
o fix the issue invloved by replace class(x)=="something" to is(x, "something").
CHANGES IN VERSION 1.29.8
-----------------------
o remove google scholar from vignette.
CHANGES IN VERSION 1.29.7
-----------------------
o Add google scholar in vignette.
CHANGES IN VERSION 1.29.6
-----------------------
o fix a bug that 'grid' and 'graphics' output mixed for plotMotifStackWithPhylog
CHANGES IN VERSION 1.29.5
-----------------------
o fix a bug that importMatrix can not handle empty matrix.
CHANGES IN VERSION 1.29.4
-----------------------
o fix a bug that markers shift position when alignment.
CHANGES IN VERSION 1.29.3
-----------------------
o accept pcm for plotMotifLogoA
o geom_motif accept x,y,width,height
CHANGES IN VERSION 1.29.2
-----------------------
o add markers
CHANGES IN VERSION 1.29.1
-----------------------
o add function geom_motif
CHANGES IN VERSION 1.27.5
-----------------------
o change plotMotifLogo to grob.
CHANGES IN VERSION 1.27.4
-----------------------
o Update authors information.
o change the d3-tip background color.
o adjust the fontsize to remove the gaps.
o change the title position.
CHANGES IN VERSION 1.27.3
-----------------------
o use grImport2 instead grImport to avoid the installation of ghostscript.
CHANGES IN VERSION 1.27.2
-----------------------
o add knitr in vignettes to pass window's builder
CHANGES IN VERSION 1.27.1
-----------------------
o try to pass window's builder
CHANGES IN VERSION 1.25.2
-----------------------
o fix the bug when plot "others" type of motif.
CHANGES IN VERSION 1.25.1
-----------------------
o Fix a bug for y-axis plot.
CHANGES IN VERSION 1.23.12
-----------------------
o Silence importMatrix for scan.
CHANGES IN VERSION 1.23.11
-----------------------
o Fix the bug in importMatrix for meme files.
CHANGES IN VERSION 1.23.10
-----------------------
o Fix the bug in importMatrix for meme files.
CHANGES IN VERSION 1.23.9
-----------------------
o Fix the warning in windows.
CHANGES IN VERSION 1.23.8
-----------------------
o Update the documentation plotMotifStackWithRadialPhylog.
CHANGES IN VERSION 1.23.7
-----------------------
o Update vignette.
CHANGES IN VERSION 1.23.6
-----------------------
o Add citation.
CHANGES IN VERSION 1.23.5
-----------------------
o Update authors email.
CHANGES IN VERSION 1.23.4
-----------------------
o create global environment to save tmp values.
CHANGES IN VERSION 1.23.3
-----------------------
o change the colorset name from colorBlindness to blindnessSafe
CHANGES IN VERSION 1.23.2
-----------------------
o fix some bugs in documentation.
CHANGES IN VERSION 1.23.1
-----------------------
o add a new color set for color blind safe.
CHANGES IN VERSION 1.21.7
-----------------------
o add newline at the end of RUNX1.pfm
CHANGES IN VERSION 1.21.6
-----------------------
o update the documentations
CHANGES IN VERSION 1.21.5
-----------------------
o add class psam
o add function plotAffinityLogo
CHANGES IN VERSION 1.21.4
-----------------------
o add function importMatrix
CHANGES IN VERSION 1.21.3
-----------------------
o add one more option for motifPiles and motifCircos
CHANGES IN VERSION 1.21.2
-----------------------
o fix a bug in plotMotifLogo for pcm
CHANGES IN VERSION 1.21.1
-----------------------
o update the vignettes.
CHANGES IN VERSION 1.19.4
-----------------------
NEW FEATURES
o update the css file for tooltip to function browseMotifs.
CHANGES IN VERSION 1.19.3
-----------------------
NEW FEATURES
o add tooltip to function browseMotifs.
CHANGES IN VERSION 1.19.2
-----------------------
NEW FEATURES
o add radialPhylog layout to function browseMotifs.
CHANGES IN VERSION 1.19.1
-----------------------
NEW FEATURES
o add new function browseMotifs.
CHANGES IN VERSION 1.13.8
-----------------------
NEW FEATURES
o improve plot plotMotifStackWithPhylog.
CHANGES IN VERSION 1.13.7
-----------------------
o update the documentation
CHANGES IN VERSION 1.13.6
-----------------------
BUG FIXES
o fix bug when plot 2 motifs with motifStack function.
CHANGES IN VERSION 1.13.5
-----------------------
NEW FEATURES
o improve the algorithm of DNAmotifAlignment. Replaced the ALLR by average
information content.
CHANGES IN VERSION 1.13.4
-----------------------
NEW FEATURES
o improve the algorithm of DNAmotifAlignment
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.13.3
-----------------------
NEW FEATURES
o add reorderUPGMAtree function
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.13.2
-----------------------
NEW FEATURES
o add mergeMotifs function
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.13.1
-----------------------
NEW FEATURES
o add plotMotifOverMotif function
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.11.8
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o Fix the bugs if background values don't have a name.
CHANGES IN VERSION 1.11.7
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o Fix the bugs in readPWM
CHANGES IN VERSION 1.11.6
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o Fix the bugs in motifCircos when input r.pfm and r.pfm2
CHANGES IN VERSION 1.11.5
-----------------------
NEW FEATURES
o export $ and $<- methods for classes
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.11.4
-----------------------
NEW FEATURES
o add function getRankedUniqueMotifs and pfm2pwm
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.11.3
-----------------------
NEW FEATURES
o add function motifPiles
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.11.2
-----------------------
NEW FEATURES
o export function highlightCol
o add function motifCircos
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.11.1
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o Change the format of help file to avoid lines wider than 90 characters NOTE
CHANGES IN VERSION 1.9.9
-----------------------
NEW FEATURES
o Add distance axis for plotMotifStackWithRadiaPhylog
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.9.8
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o fix the bug draw motif outside of canvas when plotMotifStackWithRadiaPhylog
CHANGES IN VERSION 1.9.7
-----------------------
NEW FEATURES
o Change the position of motifs index when plotMotifStackWithRadialPhylog.
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.9.6
-----------------------
NEW FEATURES
o Increase the size of motifs when plotMotifStackWithRadialPhylog.
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.9.5
-----------------------
NEW FEATURES
o Change default of plotIndex to FALSE when plotMotifStackWithRadialPhylog.
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.9.4
-----------------------
NEW FEATURES
o Restyle index number when plotMotifStackWithRadialPhylog.
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.9.3
-----------------------
NEW FEATURES
o Add index number when plotMotifStackWithRadialPhylog.
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.9.2
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o Fix bugs using motifDB in tests.
CHANGES IN VERSION 1.7.8
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o Fix bugs for motifSignature when the distance is larger than
maximal distance.
CHANGES IN VERSION 1.7.7
-----------------------
NEW FEATURES
o add ic.scale parameter to plotMotifLogo.
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.7.6
-----------------------
NEW FEATURES
o Change the class of signature to include the color sets.
BUG FIXES
o Allow motifSignature to accept Non-Binary Trees.
CHANGES IN VERSION 1.7.5
-----------------------
NEW FEATURES
o Change the output of motifStack for further steps.
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.7.3
-----------------------
NEW FEATURES
o Change the output of readPCM from a matrix to a list of
pcm objects.
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.7.2
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o fix the bugs of changing plot layout when using plotMotifLogoStackWithTree
CHANGES IN VERSION 1.7.1
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o fix the bugs of leave names and plot region
CHANGES IN VERSION 1.5.4
-----------------------
NEW FEATURES
o use BiocStyle to write vignette
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.5.3
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o fix the bug that motifStack can not plot color correctly for
radialPhylog layout in motifStack().
CHANGES IN VERSION 1.5.2
-----------------------
NEW FEATURES
o use log-likelihood ratio (ALLR) to do alignment
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.5.1
-----------------------
NEW FEATURES
o plotMotifStackWithRadialPhylog can draw motif cloud in
RadialPhylog style. Check vignette to see the details
BUG FIXES
o check mode of pcm and pfm matrix, which should be numeric
CHANGES IN VERSION 1.2.12
-----------------------
NEW FEATURES
o New methods add to pcm and pfm class.
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.2.10
-----------------------
NEW FEATURES
o New function motifStack
o motifCloud function is separated into two functions: motifSignature
and motifCloud
o New class pcm and motifSig
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.2.9
-----------------------
NEW FEATURES
o New layout for function motifCloud to draw motif cloud
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.2.8
-----------------------
NEW FEATURES
o New function motifCloud to draw motif cloud
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.2.7
-----------------------
NEW FEATURES
o Shorten the execution time
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.2.6
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o Fix bug object 'rayonWidth' not found when the pfms is not given
for plotMotifStackWithRadialPhylog()
CHANGES IN VERSION 1.2.5
-----------------------
NEW FEATURES
o Append a set of color prameter to control
the behavior of plotMotifStackWithRadialPhylog()
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.2.4
-----------------------
NEW FEATURES
o Append a prameter clockwise, init.angle and angle to control
the behavior of plotMotifStackWithRadialPhylog()
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.2.3
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o fix the bug that plots x-axis repeatedly in plotMotifLogo().
CHANGES IN VERSION 1.2.2
-----------------------
NEW FEATURES
o Append a prameter revcomp indicates whether the DNAmotifAlignment
should use reverse-complement motif for alignment.
BUG FIXES
o Append a prameter rcpostfix, defaut is "(RC)", to the name slot
of the pfm when DNAmotifAlignment using reverse-complement motif
for alignment.
CHANGES IN VERSION 1.2.0
-----------------------
NEW FEATURES
o draw aligned motif logo stacks with phylogenetic tree in radial style
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.0.0
-----------------------
NEW FEATURES
o draw DNA/RNA sequence logo
o draw Amino Acid sequence logo
o draw aligned motif logo stacks with phylogenetic tree
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)