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motifStack (version 1.16.2)

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

1.16.2

License

GPL (>= 2)

Maintainer

Last Published

February 15th, 2017

Functions in motifStack (1.16.2)

motifPiles

plot sequence logo stacks with a linear phylogenic tree and multiple color sets
getRankedUniqueMotifs

get the unique motif in each category grouped by distance
motifSig-class

Class "motifSig"
motifStack

plot a DNA sequence logo stack
ouNode-class

Class ouNode
pcm-methods

"pcm" methods
pfm2pwm

convert pfm object to PWM
pfm-class

Class "pfm"
mergeMotifs

merge multiple motifs
pcm-class

Class "pcm"
motifSig-methods

"motifSig" methods
motifCloud

plot a DNA sequence logo cloud
plotMotifLogoStack

plot sequence logos stack
pfm-methods

"pfm" methods
motifCircos

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

plot sequence logos stack with hierarchical cluster tree
plotMotifStackWithRadialPhylog

plot sequence logo stacks with a radial phylogenic tree
motifSignature

get signatures from motifs
plotXaxis

plot x-axis
plotMotifLogo

plot sequence logo
reorderUPGMAtree

re-order UPGMA tree
plotYaxis

plot y-axis
readPCM

read pcm from a path
plotMotifStackWithPhylog

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

plot motif over another motif
DNAmotifAlignment

align DNA motifs
colorset

retrieve color setting for logo
motifStack-package

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

plot sequence logo without plot.new
highlightCol

add alpha transparency value to a color