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

## Documentation for package ‘motifStack’ version 1.55.0

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

## Help Pages

A B C D F G H I M N O P R S T misc

motifStack-package | Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

## -- A --

AAmotifAlignment | align AA motifs
addBlank | Class '"pcm"'
addBlank-method | Class '"pcm"'
addBlank-method | Class '"pfm"'
addBlank-method | Class '"psam"'
addBlank-method | Class '"pssm"'
as | Class '"pcm"'
as() | Class '"psam"'
as.data.frame-method | Class '"pcm"'
as.data.frame-method | Class '"pfm"'
as.data.frame-method | Class '"psam"'
as.data.frame-method | Class '"pssm"'

## -- B --

browseMotifs | browse motifs
browseMotifs-shiny | Shiny bindings for browseMotifs
browseMotifsOutput | Shiny bindings for browseMotifs

## -- C --

calF | calculate frequence
calI | calculate I'
clusterMotifs | cluster motifs
coerce | Class '"pfm"'
coerce() | Class '"pssm"'
coerce-method | Class '"pcm"'
coerce-method | Class '"pfm"'
coerce-method | Class '"psam"'
coerce-method | Class '"pssm"'
colorset | retrieve color setting for logo
compare2profiles | compare two profiles
compareProfiles | comapre w pcm

## -- D --

DNAmotifAlignment | align DNA motifs
DNAmotifToRNAmotif | convert DNA motif into RNA motif
dpGlobal | Global alignment version
dpLocal | Dynamic programming function, local version

## -- F --

format-method | Class '"pcm"'
format-method | Class '"pfm"'
format-method | Class '"psam"'
format-method | Class '"pssm"'
frequence | Class '"motifSig"'
frequence-method | Class '"motifSig"'

## -- G --

GeomMotif | GeomMotif object
geom_motif | geom_motif
getALLRscoreFromCounts | calculate ALLR from counts
getDistance | Calculate distances between two profiles
getIC | Class '"pcm"'
getIC-method | Class '"pcm"'
getIC-method | Class '"pfm"'
getRankedUniqueMotifs | get the unique motif in each category grouped by distance
getScore | Calculate pair_wise position score

## -- H --

highlightCol | add alpha transparency value to a color

## -- I --

importMatrix | import motifs from local files

## -- M --

marker | Class 'marker'
marker-class | Class 'marker'
matalign | Matrix Aligner
matrixReverseComplement | Class '"pcm"'
matrixReverseComplement-method | Class '"pcm"'
matrixReverseComplement-method | Class '"pfm"'
matrixReverseComplement-method | Class '"psam"'
matrixReverseComplement-method | Class '"pssm"'
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
motifGrob | Motif Grob
motifHclust | Hierarchical Clustering motifs
motifPiles | plot sequence logo stacks with a linear phylogenic tree and multiple color sets
motifSig | Class '"motifSig"'
motifSig-class | Class '"motifSig"'
motifSignature | get signatures from motifs
motifStack | plot a DNA sequence logo stack

## -- N --

nodelist | Class '"motifSig"'
nodelist-method | Class '"motifSig"'

## -- O --

ouNode | Class 'ouNode'
ouNode-class | Class 'ouNode'

## -- P --

pcm | Class '"pcm"'
pcm-class | Class '"pcm"'
pcm2pfm | Class '"pcm"'
pcm2pfm-method | Class '"pcm"'
pcm2pssm | Class '"pcm"'
pcm2pssm-method | Class '"pcm"'
pfm | Class '"pfm"'
pfm-class | Class '"pfm"'
pfm2pwm | convert pfm object to PWM
plot | Class '"pcm"'
plot-method | Class '"pcm"'
plot-method | Class '"pfm"'
plot-method | Class '"psam"'
plot-method | Class '"pssm"'
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 | Class '"psam"'
psam-class | Class '"psam"'
pssm | Class '"pssm"'
pssm-class | Class '"pssm"'

## -- R --

readPCM | read pcm from a path
renderbrowseMotifs | Shiny bindings for browseMotifs
reorderUPGMAtree | re-order UPGMA tree

## -- S --

sigColor | Class '"motifSig"'
sigColor-method | Class '"motifSig"'
signatures | Class '"motifSig"'
signatures-method | Class '"motifSig"'

## -- T --

traceBackGlobal | traceback global
traceBackLocal | traceback local
trimMotif | Class '"pcm"'
trimMotif-method | Class '"pcm"'
trimMotif-method | Class '"pfm"'

## -- misc --

$-method | Class 'marker'
$-method | Class '"motifSig"'
$-method | Class 'ouNode'
$-method | Class '"pcm"'
$-method | Class '"pfm"'
$-method | Class '"psam"'
$-method | Class '"pssm"'
$<--method | Class 'marker'
$<--method | Class '"motifSig"'
$<--method | Class 'ouNode'
$<--method | Class '"pcm"'
$<--method | Class '"pfm"'
$<--method | Class '"psam"'
$<--method | Class '"pssm"'