NEWS

---

motifStack 1.49.1

• Fix the issue for importMatrix when 'w' is missing.

motifStack 1.47.1

• Update documentation of motifStack function.

motifStack 1.45.1

• Fix the issue of 'This picture was not generated by Cairo graphics' for importSVG.

motifStack 1.41.1

• Fix the issue of importMatrix for mixed cases of alphabet in MEME format.

motifStack 1.39.4

• Change the fontfamily from 'mono,Courier' to 'mono' in vignettes.

motifStack 1.39.3

• add XMatrix format for importMatrix.

motifStack 1.39.2

• Accept scales for y-axis for logo when ic.scale is FALSE.

motifStack 1.39.1

• Accept user defined x-axis for logo.

motifStack 1.37.5

• Change the style of motifPile.
• Fix the bug of the ylab grid.

motifStack 1.37.4

• Fix the bug that the rownames were not checked for alignment.

motifStack 1.37.3

• Fix the bug method argument of matAlign is ignored.

motifStack 1.37.2

• Improve importMatrix to read the tags from file.

motifStack 1.37.1

• handle the error "failed to load cairo DLL"

motifStack 1.35.2

• Add rmarkdown as suggest package.

motifStack 1.33.14

• remove reverse complement alignment for RNA motifs.

motifStack 1.33.13

• narrow the predefined font.

motifStack 1.33.12

• fix the issue for pcm2pfm if the column counts are not identical.

motifStack 1.33.11

• update the markers to allow label + line/rect.

motifStack 1.33.10

• add alignment function for AA motifs.

motifStack 1.33.9

• fix the issue for AA motif of clusterMotifs

motifStack 1.33.8

• fix the issue of symbol position for predefined font

motifStack 1.33.7

• update check ghostscript

motifStack 1.33.6

• fix the bug in pcm2pssm

motifStack 1.33.5

• fix the bug in pcm2pssm

motifStack 1.33.4

• add pssm class

motifStack 1.33.3

• replace MotIV by matalign.
• add cutoffPval for motifSignature function.

motifStack 1.33.2

• add parameter environment for coloredSymbols

motifStack 1.33.1

• change grImport, grImport2 and MotIV to Suggests.
• use roxygen2 to generate help files.

motifStack 1.31.2

• reduce the compiling time for vignettes.

motifStack 1.31.1

• fix the issue invloved by replace class(x)=="something" to is(x, "something").

motifStack 1.29.8

• remove google scholar from vignette.

motifStack 1.29.7

• Add google scholar in vignette.

motifStack 1.29.6

• fix a bug that 'grid' and 'graphics' output mixed for plotMotifStackWithPhylog

motifStack 1.29.5

• fix a bug that importMatrix can not handle empty matrix.

motifStack 1.29.4

• fix a bug that markers shift position when alignment.

motifStack 1.29.3

• accept pcm for plotMotifLogoA
• geom_motif accept x,y,width,height

motifStack 1.29.2

• add markers

motifStack 1.29.1

• add function geom_motif

motifStack 1.27.5

• change plotMotifLogo to grob.

motifStack 1.27.4

• Update authors information.
• change the d3-tip background color.
• adjust the fontsize to remove the gaps.
• change the title position.

motifStack 1.27.3

• use grImport2 instead grImport to avoid the installation of ghostscript.

motifStack 1.27.2

• add knitr in vignettes to pass window's builder

motifStack 1.27.1

• try to pass window's builder

motifStack 1.25.2

• fix the bug when plot "others" type of motif.

motifStack 1.25.1

• Fix a bug for y-axis plot.

motifStack 1.23.12

• Silence importMatrix for scan.

motifStack 1.23.11

• Fix the bug in importMatrix for meme files.

motifStack 1.23.10

• Fix the bug in importMatrix for meme files.

motifStack 1.23.9

• Fix the warning in windows.

motifStack 1.23.8

• Update the documentation plotMotifStackWithRadialPhylog.

motifStack 1.23.7

• Update vignette.

motifStack 1.23.6

• Add citation.

motifStack 1.23.5

• Update authors email.

motifStack 1.23.4

• create global environment to save tmp values.

motifStack 1.23.3

• change the colorset name from colorBlindness to blindnessSafe

motifStack 1.23.2

• fix some bugs in documentation.

motifStack 1.23.1

• add a new color set for color blind safe.

motifStack 1.21.7

• add newline at the end of RUNX1.pfm

motifStack 1.21.6

• update the documentations

motifStack 1.21.5

• add class psam
• add function plotAffinityLogo

motifStack 1.21.4

• add function importMatrix

motifStack 1.21.3

• add one more option for motifPiles and motifCircos

motifStack 1.21.2

• fix a bug in plotMotifLogo for pcm

motifStack 1.21.1

• update the vignettes.

motifStack 1.19.4

NEW FEATURES

• update the css file for tooltip to function browseMotifs.

motifStack 1.19.3

NEW FEATURES

• add tooltip to function browseMotifs.

motifStack 1.19.2

NEW FEATURES

• add radialPhylog layout to function browseMotifs.

motifStack 1.19.1

NEW FEATURES

• add new function browseMotifs.

motifStack 1.13.8

NEW FEATURES

• improve plot plotMotifStackWithPhylog.

motifStack 1.13.7

• update the documentation

motifStack 1.13.6

BUG FIXES

• fix bug when plot 2 motifs with motifStack function.

motifStack 1.13.5

NEW FEATURES

• improve the algorithm of DNAmotifAlignment. Replaced the ALLR by average information content.

motifStack 1.13.4

NEW FEATURES

• improve the algorithm of DNAmotifAlignment

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.13.3

NEW FEATURES

• add reorderUPGMAtree function

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.13.2

NEW FEATURES

• add mergeMotifs function

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.13.1

NEW FEATURES

• add plotMotifOverMotif function

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.11.8

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• Fix the bugs if background values don't have a name.

motifStack 1.11.7

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• Fix the bugs in readPWM

motifStack 1.11.6

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• Fix the bugs in motifCircos when input r.pfm and r.pfm2

motifStack 1.11.5

NEW FEATURES

• export $ and $<- methods for classes

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.11.4

NEW FEATURES

• add function getRankedUniqueMotifs and pfm2pwm

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.11.3

NEW FEATURES

• add function motifPiles

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.11.2

NEW FEATURES

• export function highlightCol
• add function motifCircos

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.11.1

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• Change the format of help file to avoid lines wider than 90 characters NOTE

motifStack 1.9.9

NEW FEATURES

• Add distance axis for plotMotifStackWithRadiaPhylog

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.9.8

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• fix the bug draw motif outside of canvas when plotMotifStackWithRadiaPhylog

motifStack 1.9.7

NEW FEATURES

• Change the position of motifs index when plotMotifStackWithRadialPhylog.

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.9.6

NEW FEATURES

• Increase the size of motifs when plotMotifStackWithRadialPhylog.

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.9.5

NEW FEATURES

• Change default of plotIndex to FALSE when plotMotifStackWithRadialPhylog.

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.9.4

NEW FEATURES

• Restyle index number when plotMotifStackWithRadialPhylog.

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.9.3

NEW FEATURES

• Add index number when plotMotifStackWithRadialPhylog.

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.9.2

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• Fix bugs using motifDB in tests.

motifStack 1.7.8

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• Fix bugs for motifSignature when the distance is larger than maximal distance.

motifStack 1.7.7

NEW FEATURES

• add ic.scale parameter to plotMotifLogo.

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.7.6

NEW FEATURES

• Change the class of signature to include the color sets.

BUG FIXES

• Allow motifSignature to accept Non-Binary Trees.

motifStack 1.7.5

NEW FEATURES

• Change the output of motifStack for further steps.

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.7.3

NEW FEATURES

• Change the output of readPCM from a matrix to a list of pcm objects.

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.7.2

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• fix the bugs of changing plot layout when using plotMotifLogoStackWithTree

motifStack 1.7.1

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• fix the bugs of leave names and plot region

motifStack 1.5.4

NEW FEATURES

• use BiocStyle to write vignette

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.5.3

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• fix the bug that motifStack can not plot color correctly for radialPhylog layout in motifStack().

motifStack 1.5.2

NEW FEATURES

• use log-likelihood ratio (ALLR) to do alignment

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.5.1

NEW FEATURES

• plotMotifStackWithRadialPhylog can draw motif cloud in RadialPhylog style. Check vignette to see the details

BUG FIXES

• check mode of pcm and pfm matrix, which should be numeric

motifStack 1.2.12

NEW FEATURES

• New methods add to pcm and pfm class.

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.2.10

NEW FEATURES

• New function motifStack
• motifCloud function is separated into two functions: motifSignature and motifCloud
• New class pcm and motifSig

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.2.9

NEW FEATURES

• New layout for function motifCloud to draw motif cloud

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.2.8

NEW FEATURES

• New function motifCloud to draw motif cloud

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.2.7

NEW FEATURES

• Shorten the execution time

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.2.6

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• Fix bug object 'rayonWidth' not found when the pfms is not given for plotMotifStackWithRadialPhylog()

motifStack 1.2.5

NEW FEATURES

• Append a set of color prameter to control the behavior of plotMotifStackWithRadialPhylog()

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.2.4

NEW FEATURES

• Append a prameter clockwise, init.angle and angle to control the behavior of plotMotifStackWithRadialPhylog()

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.2.3

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• fix the bug that plots x-axis repeatedly in plotMotifLogo().

motifStack 1.2.2

NEW FEATURES

• Append a prameter revcomp indicates whether the DNAmotifAlignment should use reverse-complement motif for alignment.

BUG FIXES

• Append a prameter rcpostfix, defaut is "(RC)", to the name slot of the pfm when DNAmotifAlignment using reverse-complement motif for alignment.

motifStack 1.2.0

NEW FEATURES

• draw aligned motif logo stacks with phylogenetic tree in radial style

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

motifStack 1.0.0

NEW FEATURES

• draw DNA/RNA sequence logo
• draw Amino Acid sequence logo
• draw aligned motif logo stacks with phylogenetic tree

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)