Changes in version 1.53.2 o Speedup motifHclust Changes in version 1.53.1 o Support import Hocomoco format. 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. 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)