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

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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.

Author
Jianhong Ou, Michael Brodsky, Scot Wolfe and Lihua Julie Zhu
Date of publication
None
Maintainer
Jianhong Ou <jianhong.ou@umassmed.edu>
License
GPL (>= 2)
Version
1.18.0

View on Bioconductor

Man pages

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

Files in this package

motifStack/DESCRIPTION
motifStack/NAMESPACE
motifStack/NEWS
motifStack/R
motifStack/R/getRankedUniqueMotifs.R
motifStack/R/mergeMotifs.R
motifStack/R/motifCircos.R
motifStack/R/motifPiles.R
motifStack/R/motifStack.R
motifStack/R/pcm.R
motifStack/R/pfm.R
motifStack/R/plotMotifOverMotif.R
motifStack/R/privateUtilities.R
motifStack/R/publicUtilities.R
motifStack/R/reorderUPGMAtree.R
motifStack/R/signature.R
motifStack/build
motifStack/build/vignette.rds
motifStack/inst
motifStack/inst/doc
motifStack/inst/doc/motifStack.R
motifStack/inst/doc/motifStack.Rnw
motifStack/inst/doc/motifStack.pdf
motifStack/inst/doc/motifStack_HTML.R
motifStack/inst/doc/motifStack_HTML.Rmd
motifStack/inst/doc/motifStack_HTML.html
motifStack/inst/extdata
motifStack/inst/extdata/FoxP_SOLEXA.pcm
motifStack/inst/extdata/bin_SOLEXA.pcm
motifStack/inst/extdata/cap.txt
motifStack/inst/extdata/fd64A_SOLEXA.pcm
motifStack/inst/extdata/fkh_NAR.pcm
motifStack/inst/extdata/foxo_SOLEXA.pcm
motifStack/inst/extdata/slp1_SOLEXA.pcm
motifStack/inst/extdata/slp2_SOLEXA.pcm
motifStack/inst/unitTests
motifStack/inst/unitTests/test_motifStack.R
motifStack/man
motifStack/man/DNAmotifAlignment.Rd
motifStack/man/colorset.Rd
motifStack/man/getRankedUniqueMotifs.Rd
motifStack/man/highlightCol.Rd
motifStack/man/mergeMotifs.Rd
motifStack/man/motifCircos.Rd
motifStack/man/motifCloud.Rd
motifStack/man/motifPiles.Rd
motifStack/man/motifSig-class.Rd
motifStack/man/motifSig-methods.Rd
motifStack/man/motifSignature.Rd
motifStack/man/motifStack-package.Rd
motifStack/man/motifStack.Rd
motifStack/man/ouNode-class.Rd
motifStack/man/pcm-class.Rd
motifStack/man/pcm-methods.Rd
motifStack/man/pfm-class.Rd
motifStack/man/pfm-methods.Rd
motifStack/man/pfm2pwm.Rd
motifStack/man/plotMotifLogo.Rd
motifStack/man/plotMotifLogoA.Rd
motifStack/man/plotMotifLogoStack.Rd
motifStack/man/plotMotifLogoStackWithTree.Rd
motifStack/man/plotMotifOverMotif.Rd
motifStack/man/plotMotifStackWithPhylog.Rd
motifStack/man/plotMotifStackWithRadialPhylog.Rd
motifStack/man/plotXaxis.Rd
motifStack/man/plotYaxis.Rd
motifStack/man/readPCM.Rd
motifStack/man/reorderUPGMAtree.Rd
motifStack/tests
motifStack/tests/runTests.R
motifStack/vignettes
motifStack/vignettes/motifStack.Rnw
motifStack/vignettes/motifStack_HTML.Rmd
motifStack/vignettes/ref.bib