motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Version 1.20.0

The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.

Browse man pages Browse package API and functions Browse package files

AuthorJianhong Ou, Michael Brodsky, Scot Wolfe and Lihua Julie Zhu
Bioconductor views Alignment ChIPSeq ChIPchip DataImport Microarray MotifAnnotation SequenceMatching Sequencing Visualization
Date of publicationNone
MaintainerJianhong Ou <jianhong.ou@umassmed.edu>
LicenseGPL (>= 2)
Version1.20.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("motifStack")

Man pages

browseMotifs: browse motifs
browseMotifs-shiny: Shiny bindings for browseMotifs
colorset: retrieve color setting for logo
DNAmotifAlignment: align DNA motifs
getRankedUniqueMotifs: get the unique motif in each category grouped by distance
highlightCol: add alpha transparency value to a color
mergeMotifs: merge multiple motifs
motifCircos: plot sequence logo stacks with a radial phylogenic tree and...
motifCloud: plot a DNA sequence logo cloud
motifPiles: plot sequence logo stacks with a linear phylogenic tree and...
motifSig-class: Class '"motifSig"'
motifSig-methods: "motifSig" methods
motifSignature: get signatures from motifs
motifStack: plot a DNA sequence logo stack
motifStack-package: Plot stacked logos for single or multiple DNA, RNA and amino...
ouNode-class: Class 'ouNode'
pcm-class: Class '"pcm"'
pcm-methods: "pcm" methods
pfm2pwm: convert pfm object to PWM
pfm-class: Class '"pfm"'
pfm-methods: "pfm" methods
plotMotifLogo: plot sequence logo
plotMotifLogoA: plot sequence logo without plot.new
plotMotifLogoStack: plot sequence logos stack
plotMotifLogoStackWithTree: plot sequence logos stack with hierarchical cluster tree
plotMotifOverMotif: plot motif over another motif
plotMotifStackWithPhylog: plot sequence logo stacks with a ape4-style phylogenic tree
plotMotifStackWithRadialPhylog: plot sequence logo stacks with a radial phylogenic tree
plotXaxis: plot x-axis
plotYaxis: plot y-axis
readPCM: read pcm from a path
reorderUPGMAtree: re-order UPGMA tree

Functions

$,motifSig-method Man page
$,ouNode-method Man page
$,pcm-method Man page
$,pfm-method Man page
$<-,motifSig-method Man page
$<-,ouNode-method Man page
$<-,pcm-method Man page
$<-,pfm-method Man page
DNAmotifAlignment Man page Source code
SWU Source code
UngappedAlignment Source code
addBlank Man page
addBlank,pcm,numeric,logical-method Man page
addBlank,pfm,numeric,logical-method Man page
addPseudolog2 Source code
browseMotifs Man page Source code
browseMotifs-shiny Man page
browseMotifsOutput Man page Source code
checkALLR Source code
checkInteger Source code
coloredSymbols Source code
colorset Man page Source code
frequence Man page
frequence,motifSig-method Man page
getALLRbyBase Source code
getAlignedICWithoutGap Source code
getHomoDimerCenter Source code
getIC Man page
getIC,matrix,matrix-method Man page
getIC,matrix,numeric-method Man page
getIC,pcm,ANY-method Man page
getIC,pfm,ANY-method Man page
getICbyBase Source code
getIE Source code
getPFMid Source code
getParentNode Source code
getRankedUniqueMotifs Man page Source code
getoffsetPosByIC Source code
getoffsetPosByIC_old Source code
hex2psrgb Source code
highlightCol Man page Source code
isHomoDimer Source code
makeLeaveNames Source code
matrixReverseComplement Man page
matrixReverseComplement,pcm-method Man page
matrixReverseComplement,pfm-method Man page
mergeMotifs Man page Source code
motifCircos Man page Source code
motifCloud Man page Source code
motifPiles Man page Source code
motifSig Man page
motifSig-class Man page
motifSignature Man page Source code
motifStack Man page Source code
motifStack-package Man page
nodelist Man page
nodelist,motifSig-method Man page
ouNode Man page
ouNode-class Man page
pcm Man page
pcm-class Man page
pcm2pfm Man page
pcm2pfm,data.frame,ANY-method Man page
pcm2pfm,data.frame,numeric-method Man page
pcm2pfm,matrix,ANY-method Man page
pcm2pfm,matrix,numeric-method Man page
pcm2pfm,pcm,ANY-method Man page
pfm Man page
pfm-class Man page
pfm2pwm Man page Source code
plot,pcm,ANY-method Man page
plot,pfm,ANY-method Man page
plotMotifLogo Man page Source code
plotMotifLogoA Man page Source code
plotMotifLogoStack Man page Source code
plotMotifLogoStackWithTree Man page Source code
plotMotifOverMotif Man page Source code
plotMotifStackWithPhylog Man page Source code
plotMotifStackWithRadialPhylog Man page Source code
plotXaxis Man page Source code
plotYaxis Man page Source code
readPCM Man page Source code
readPWM Source code
renderbrowseMotifs Man page Source code
reorderUPGMAtree Man page Source code
sigColor Man page
sigColor,motifSig-method Man page
signatures Man page
signatures,motifSig-method Man page
trimMotif Man page
trimMotif,pcm,numeric-method Man page
trimMotif,pfm,numeric-method Man page
ungappedScore Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/browseMotifs.R
R/getRankedUniqueMotifs.R
R/mergeMotifs.R
R/motifCircos.R
R/motifPiles.R
R/motifStack.R
R/pcm.R
R/pfm.R
R/plotMotifOverMotif.R
R/privateUtilities.R
R/publicUtilities.R
R/reorderUPGMAtree.R
R/signature.R
build
build/vignette.rds
inst
inst/doc
inst/doc/motifStack.R
inst/doc/motifStack.Rnw
inst/doc/motifStack.pdf
inst/doc/motifStack_HTML.R
inst/doc/motifStack_HTML.Rmd
inst/doc/motifStack_HTML.html
inst/extdata
inst/extdata/FoxP_SOLEXA.pcm
inst/extdata/bin_SOLEXA.pcm
inst/extdata/cap.txt
inst/extdata/fd64A_SOLEXA.pcm
inst/extdata/fkh_NAR.pcm
inst/extdata/foxo_SOLEXA.pcm
inst/extdata/slp1_SOLEXA.pcm
inst/extdata/slp2_SOLEXA.pcm
inst/htmlwidgets
inst/htmlwidgets/browseMotifs.js
inst/htmlwidgets/browseMotifs.yaml
inst/htmlwidgets/lib
inst/htmlwidgets/lib/d3
inst/htmlwidgets/lib/d3-tip
inst/htmlwidgets/lib/d3-tip/d3-tip.css
inst/htmlwidgets/lib/d3-tip/d3-tip.js
inst/htmlwidgets/lib/d3/d3.v4.min.js
inst/htmlwidgets/lib/plotWebLogo
inst/htmlwidgets/lib/plotWebLogo/d3-plotWebLogo.css
inst/htmlwidgets/lib/plotWebLogo/d3-plotWebLogo.js
inst/htmlwidgets/lib/saveSvgAsPng
inst/htmlwidgets/lib/saveSvgAsPng/saveSvgAsPng.js
inst/unitTests
inst/unitTests/test_motifStack.R
man
man/DNAmotifAlignment.Rd
man/browseMotifs-shiny.Rd
man/browseMotifs.Rd
man/colorset.Rd
man/getRankedUniqueMotifs.Rd
man/highlightCol.Rd
man/mergeMotifs.Rd
man/motifCircos.Rd
man/motifCloud.Rd
man/motifPiles.Rd
man/motifSig-class.Rd
man/motifSig-methods.Rd
man/motifSignature.Rd
man/motifStack-package.Rd
man/motifStack.Rd
man/ouNode-class.Rd
man/pcm-class.Rd
man/pcm-methods.Rd
man/pfm-class.Rd
man/pfm-methods.Rd
man/pfm2pwm.Rd
man/plotMotifLogo.Rd
man/plotMotifLogoA.Rd
man/plotMotifLogoStack.Rd
man/plotMotifLogoStackWithTree.Rd
man/plotMotifOverMotif.Rd
man/plotMotifStackWithPhylog.Rd
man/plotMotifStackWithRadialPhylog.Rd
man/plotXaxis.Rd
man/plotYaxis.Rd
man/readPCM.Rd
man/reorderUPGMAtree.Rd
tests
tests/runTests.R
vignettes
vignettes/motifStack.Rnw
vignettes/motifStack_HTML.Rmd
vignettes/ref.bib
motifStack documentation built on May 20, 2017, 9:36 p.m.