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)