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

## Documentation for package ‘motifStack’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

motifStack-package | Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
$-method | "motifSig" methods
$-method | Class 'ouNode'
$-method | "pcm" methods
$-method | "pfm" methods
$-method | "psam" methods
$<--method | "motifSig" methods
$<--method | Class 'ouNode'
$<--method | "pcm" methods
$<--method | "pfm" methods
$<--method | "psam" methods
addBlank | "pfm" methods
addBlank-method | "pcm" methods
addBlank-method | "pfm" methods
addBlank-method | "psam" methods
browseMotifs | browse motifs
browseMotifs-shiny | Shiny bindings for browseMotifs
browseMotifsOutput | Shiny bindings for browseMotifs
colorset | retrieve color setting for logo
DNAmotifAlignment | align DNA motifs
frequence | "motifSig" methods
frequence-method | "motifSig" methods
getIC | "pfm" methods
getIC-method | "pcm" methods
getIC-method | "pfm" methods
getRankedUniqueMotifs | get the unique motif in each category grouped by distance
highlightCol | add alpha transparency value to a color
importMatrix | import motifs from local files
matrixReverseComplement | "pfm" methods
matrixReverseComplement-method | "pcm" methods
matrixReverseComplement-method | "pfm" methods
matrixReverseComplement-method | "psam" methods
mergeMotifs | merge multiple motifs
motifCircos | plot sequence logo stacks with a radial phylogenic tree and multiple color rings
motifCloud | plot a DNA sequence logo cloud
motifPiles | plot sequence logo stacks with a linear phylogenic tree and multiple color sets
motifSig | "motifSig" methods
motifSig-class | Class '"motifSig"'
motifSignature | get signatures from motifs
motifStack | plot a DNA sequence logo stack
nodelist | "motifSig" methods
nodelist-method | "motifSig" methods
ouNode | Class 'ouNode'
ouNode-class | Class 'ouNode'
pcm | "pcm" methods
pcm-class | Class '"pcm"'
pcm2pfm | "pcm" methods
pcm2pfm-method | "pcm" methods
pfm | "pfm" methods
pfm-class | Class '"pfm"'
pfm2pwm | convert pfm object to PWM
plot-method | "pcm" methods
plot-method | "pfm" methods
plot-method | "psam" methods
plotAffinityLogo | plot affinity logo
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
psam | "psam" methods
psam-class | Class '"psam"'
readPCM | read pcm from a path
renderbrowseMotifs | Shiny bindings for browseMotifs
reorderUPGMAtree | re-order UPGMA tree
sigColor | "motifSig" methods
sigColor-method | "motifSig" methods
signatures | "motifSig" methods
signatures-method | "motifSig" methods
trimMotif | "pcm" methods
trimMotif-method | "pcm" methods
trimMotif-method | "pfm" methods