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motifStack (version 1.16.0)

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

Description

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.

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Version

Version

1.16.0

License

GPL (>= 2)

Maintainer

Jianhong Ou

Last Published

February 15th, 2017

Functions in motifStack (1.16.0)

motifCloud

plot a DNA sequence logo cloud
colorset

retrieve color setting for logo
DNAmotifAlignment

align DNA motifs
pfm-class

Class "pfm"
pfm-methods

"pfm" methods
plotXaxis

plot x-axis
plotYaxis

plot y-axis
readPCM

read pcm from a path
reorderUPGMAtree

re-order UPGMA tree
mergeMotifs

merge multiple motifs
pfm2pwm

convert pfm object to PWM
plotMotifLogo

plot sequence logo
motifCircos

plot sequence logo stacks with a radial phylogenic tree and multiple color rings
motifPiles

plot sequence logo stacks with a linear phylogenic tree and multiple color sets
ouNode-class

Class ouNode
motifStack

plot a DNA sequence logo stack
plotMotifOverMotif

plot motif over another motif
plotMotifLogoStackWithTree

plot sequence logos stack with hierarchical cluster tree
motifSig-methods

"motifSig" methods
motifSig-class

Class "motifSig"
pcm-class

Class "pcm"
pcm-methods

"pcm" methods
plotMotifStackWithPhylog

plot sequence logo stacks with a ape4-style phylogenic tree
plotMotifStackWithRadialPhylog

plot sequence logo stacks with a radial phylogenic tree
getRankedUniqueMotifs

get the unique motif in each category grouped by distance
highlightCol

add alpha transparency value to a color
motifSignature

get signatures from motifs
motifStack-package

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

plot sequence logo without plot.new
plotMotifLogoStack

plot sequence logos stack