Package 'motifStack' reference manual

Title:	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.
Authors:	Jianhong Ou, Michael Brodsky, Scot Wolfe and Lihua Julie Zhu
Maintainer:	Jianhong Ou <[email protected]>
License:	GPL (>= 2)
Version:	1.49.1
Built:	2024-07-06 02:31:15 UTC
Source:	https://github.com/bioc/motifStack

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

Description

motifStack is a package that is able to draw amino acid sequence as easy as to draw DNA/RNA sequence. motifStack provides the flexibility for users to select the font type and symbol colors. motifStack is designed for graphical representation of multiple motifs.

Author(s)

Jianhong Ou and Lihua Julie Zhu

Maintainer: Jianhong Ou <[email protected]>

align AA motifs

Description

align AA motifs for plotting motifs stack

Usage

AAmotifAlignment(pcms, threshold = 0.4, minimalConsensus = 0)
AAmotifAlignment(pcms, threshold = 0.4, minimalConsensus = 0)

Arguments

`pcms`	a list of position frequency matrices, pfms must be a list of class pcm
`threshold`	information content cutoff threshold for useful postions
`minimalConsensus`	minimal length of consensus for alignment

Value

a list of aligned motifs

Examples


pcms<-importMatrix(system.file("extdata", "prot.meme", package="motifStack"),
                   format="meme", to="pfm")
motifs<-AAmotifAlignment(pcms)

pcms<-importMatrix(system.file("extdata", "prot.meme", package="motifStack"),
                   format="meme", to="pfm")
motifs<-AAmotifAlignment(pcms)

browse motifs

Description

browse motifs in a web browser

Usage

browseMotifs(
  pfms,
  phylog,
  layout = c("tree", "cluster", "radialPhylog"),
  nodeRadius = 2.5,
  baseWidth = 12,
  baseHeight = 30,
  xaxis = TRUE,
  yaxis = TRUE,
  width = NULL,
  height = NULL,
  ...
)
browseMotifs(
  pfms,
  phylog,
  layout = c("tree", "cluster", "radialPhylog"),
  nodeRadius = 2.5,
  baseWidth = 12,
  baseHeight = 30,
  xaxis = TRUE,
  yaxis = TRUE,
  width = NULL,
  height = NULL,
  ...
)

Arguments

`pfms`	a list of pfm
`phylog`	layout type. see GraphvizLayouts
`layout`	layout type. Could be tree, cluster or radialPhylog.
`nodeRadius`	node radius, default 2.5px.
`baseWidth`, `baseHeight`	width and height of each alphabet of the motif logo.
`xaxis`, `yaxis`	plot x-axis or y-axis or not in the motifs.
`width`	width of the figure
`height`	height of the figure
`...`	parameters not used

Value

An object of class htmlwidget that will intelligently print itself into HTML in a variety of contexts including the R console, within R Markdown documents, and within Shiny output bindings.

Examples


if(interactive() || Sys.getenv("USER")=="jianhongou"){
 library("MotifDb")
 matrix.fly <- query(MotifDb, "Dmelanogaster")
 motifs <- as.list(matrix.fly)
 motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                        names(motifs), fixed=TRUE)]
 names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                      gsub("_FBgn[0-9]+$", "", 
                           gsub("[^a-zA-Z0-9]","_", 
                                gsub("(_[0-9]+)+$", "", names(motifs)))))
 motifs <- motifs[unique(names(motifs))]
 pfms <- sample(motifs, 10)
 pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                  new("pfm",mat=.ele, name=.name)})
 browseMotifs(pfms)
}

if(interactive() || Sys.getenv("USER")=="jianhongou"){
 library("MotifDb")
 matrix.fly <- query(MotifDb, "Dmelanogaster")
 motifs <- as.list(matrix.fly)
 motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                        names(motifs), fixed=TRUE)]
 names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                      gsub("_FBgn[0-9]+$", "", 
                           gsub("[^a-zA-Z0-9]","_", 
                                gsub("(_[0-9]+)+$", "", names(motifs)))))
 motifs <- motifs[unique(names(motifs))]
 pfms <- sample(motifs, 10)
 pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                  new("pfm",mat=.ele, name=.name)})
 browseMotifs(pfms)
}

Shiny bindings for browseMotifs

Description

Output and render functions for using browseMotifs within Shiny applications and interactive Rmd documents.

Usage

browseMotifsOutput(outputId, width = "100%", height = "400px")

renderbrowseMotifs(expr, env = parent.frame(), quoted = FALSE)
browseMotifsOutput(outputId, width = "100%", height = "400px")

renderbrowseMotifs(expr, env = parent.frame(), quoted = FALSE)

Arguments

`outputId`	output variable to read from
`width`, `height`	Must be a valid CSS unit (like `'100%'`, `'400px'`, `'auto'`) or a number, which will be coerced to a string and have `'px'` appended.
`expr`	An expression that generates a browseMotifs
`env`	The environment in which to evaluate `expr`.
`quoted`	Is `expr` a quoted expression (with `quote()`)? This is useful if you want to save an expression in a variable.

calculate frequence

Description

calculate frequence

Usage

calF(count, P = rep(1/length(count), length(count)), pseudo = 1)
calF(count, P = rep(1/length(count), length(count)), pseudo = 1)

Arguments

`count`	position counts
`P`	background probility
`pseudo`	pseudocount

Value

numeric(1)

calculate I'

Description

calculate I'

Usage

calI(freq1, freq2, P)
calI(freq1, freq2, P)

Arguments

`freq1`	position frequence for matrix 1 position j
`freq2`	position frequence for matrix 2 position j
`P`	background of profile1

Value

numeric(1)

cluster motifs

Description

A help function to do matalign and motifHclust in one function.

Usage

clusterMotifs(motifs, ...)
clusterMotifs(motifs, ...)

Arguments

`motifs`	A list of pcms of pfms.
`...`	parameter to be passed to matalign function.

Value

An object of hclust.

Examples

 if(interactive() || Sys.getenv("USER")=="jianhongou"){
  fp <- system.file("extdata", package="motifStack")
  fs <- dir(fp, "pcm$")
  pcms <- importMatrix(file.path(fp, fs), format="pcm")
  hc <- clusterMotifs(pcms)
 }
if(interactive() || Sys.getenv("USER")=="jianhongou"){
  fp <- system.file("extdata", package="motifStack")
  fs <- dir(fp, "pcm$")
  pcms <- importMatrix(file.path(fp, fs), format="pcm")
  hc <- clusterMotifs(pcms)
 }

retrieve color setting for logo

Description

retrieve color setting for logo

Usage

colorset(alphabet = "DNA", colorScheme = "auto")
colorset(alphabet = "DNA", colorScheme = "auto")

Arguments

`alphabet`	character, 'DNA', 'RNA' or 'AA'
`colorScheme`	'auto', 'charge', 'chemistry', 'classic' or 'hydrophobicity' for AA, 'auto', 'basepairing', or 'blindnessSafe' for DNA ro RNA

Value

A character vector of color scheme

Examples


col <- colorset("AA", "hydrophobicity")

col <- colorset("AA", "hydrophobicity")

compare two profiles

Description

compare two pcm object

Usage

compare2profiles(
  pcm1,
  pcm2,
  method = c("Smith-Waterman", "Needleman-Wunsch"),
  pseudo = 1
)
compare2profiles(
  pcm1,
  pcm2,
  method = c("Smith-Waterman", "Needleman-Wunsch"),
  pseudo = 1
)

Arguments

`pcm1`, `pcm2`	object of pcm
`method`	Alignment method. "Smith-Waterman" or "Needleman-Wunsch". Default is "Smith-Waterma"
`pseudo`	pseudocount

Value

a list with names: motif1, motif2, alignmentScore, startPos1, startPos2, endPos1, endPos2, alignmentLength.

comapre w pcm

Description

compare two pcm objects

Usage

compareProfiles(
  pcm1,
  pcm2,
  method = c("Smith-Waterman", "Needleman-Wunsch"),
  pseudo = 1,
  revcomp = TRUE
)
compareProfiles(
  pcm1,
  pcm2,
  method = c("Smith-Waterman", "Needleman-Wunsch"),
  pseudo = 1,
  revcomp = TRUE
)

Arguments

`pcm1`, `pcm2`	object of pcm
`method`	Alignment method. "Smith-Waterman" or "Needleman-Wunsch". Default is "Smith-Waterma"
`pseudo`	pseudocount
`revcomp`	Check reverseComplement or not.

Value

a list with names: motif1, motif2, alignmentScore, startPos1, startPos2, endPos1, endPos2, alignmentLength.

align DNA motifs

Description

align DNA motifs for plotting motifs stack

Usage

DNAmotifAlignment(
  pfms,
  threshold = 0.4,
  minimalConsensus = 0,
  rcpostfix = "(RC)",
  revcomp = rep(TRUE, length(pfms))
)
DNAmotifAlignment(
  pfms,
  threshold = 0.4,
  minimalConsensus = 0,
  rcpostfix = "(RC)",
  revcomp = rep(TRUE, length(pfms))
)

Arguments

`pfms`	a list of position frequency matrices, pfms must be a list of class pfm or psam
`threshold`	information content cutoff threshold for useful postions
`minimalConsensus`	minimal length of consensus for alignment
`rcpostfix`	the postfix for reverse complements
`revcomp`	a logical vector to indicates whether the reverse complemet should be involved into alignment

Value

a list of aligned motifs

Examples


pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
motifs<-lapply(pcms,pcm2pfm)
motifs<-DNAmotifAlignment(motifs)

pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
motifs<-lapply(pcms,pcm2pfm)
motifs<-DNAmotifAlignment(motifs)

convert DNA motif into RNA motif

Description

convert DNA motif into RNA motif

Usage

DNAmotifToRNAmotif(pfm)
DNAmotifToRNAmotif(pfm)

Arguments

pfm

An object of "pcm" or "pfm"

Value

An object of "pcm" or "pfm" of RNA motif

Examples

motifs<-importMatrix(dir(file.path(find.package("motifStack"),
                         "extdata"),"pcm$", full.names = TRUE))
rnaMotifs <- DNAmotifToRNAmotif(motifs)
motifs<-importMatrix(dir(file.path(find.package("motifStack"),
                         "extdata"),"pcm$", full.names = TRUE))
rnaMotifs <- DNAmotifToRNAmotif(motifs)

Global alignment version

Description

Global alignment version

Usage

dpGlobal(score, m, n)
dpGlobal(score, m, n)

Arguments

`score`	ALLR scores, m x n matrix
`m`, `n`	matrix width

Value

score matrix

Dynamic programming function, local version

Description

Dynamic programming function, local version

Usage

dpLocal(score, m, n)
dpLocal(score, m, n)

Arguments

`score`	ALLR scores, m x n matrix
`m`, `n`	matrix width

Value

score matrix

geom_motif

Description

geom_motif uses the locations of the four corners (xmin, xmax, ymin and ymax) to plot motifs.

Usage

geom_motif(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  ic.scale = TRUE,
  use.xy = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)
geom_motif(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  ic.scale = TRUE,
  use.xy = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

`mapping`	Set of aesthetic mappings created by aes() or aes_(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.
`data`	The data to be displayed in this layer.
`stat`	The statistical transformation to use on the data for this layer, as a string.
`position`	Position adjustment, either as a string, or the result of a call to a position adjustment function.
`...`	Other arguments passed on to layer().
`ic.scale`	logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
`use.xy`	logical If TRUE, the required aesthethics will be x, y, width, height, and motif. Otherwise, xmin, ymin, xmax, ymax and motif.
`show.legend`	Not used.
`inherit.aes`	If FALSE, overrides the default aesthetics, rather than combining with them.

Value

a layer that contains GeomMotif object.

Aesthetics

geom_motif() understands the following aesthetics (required aesthetics are in bold):

xmin
xmax
ymin
ymax
motif
angle
fontfamily
fontface

x
y
width
height
motif
angle
fontfamily
fontface

Author(s)

Jianhong Ou

Examples


pcm <- read.table(file.path(find.package("motifStack"), 
                            "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")

df <- data.frame(xmin=c(.25, .25), ymin=c(.25, .75), xmax=c(.75, .75), ymax=c(.5, 1))
df$motif <- list(pcm2pfm(motif), pcm2pfm(motif))

library(ggplot2)
ggplot(df, aes(xmin=xmin, ymin=ymin, xmax=xmax, ymax=ymax, motif=motif)) + 
geom_motif() + theme_bw() + ylim(0, 1) + xlim(0, 1)

pcm <- read.table(file.path(find.package("motifStack"), 
                            "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")

df <- data.frame(xmin=c(.25, .25), ymin=c(.25, .75), xmax=c(.75, .75), ymax=c(.5, 1))
df$motif <- list(pcm2pfm(motif), pcm2pfm(motif))

library(ggplot2)
ggplot(df, aes(xmin=xmin, ymin=ymin, xmax=xmax, ymax=ymax, motif=motif)) + 
geom_motif() + theme_bw() + ylim(0, 1) + xlim(0, 1)

GeomMotif object

Description

GeomMotif object is a ggproto object.

Usage

GeomMotif
GeomMotif

Format

The format is: Classes 'GeoMotif', 'Geom', 'ggproto', 'gg' <ggproto object: Class GeoMotif, Geom, gg> aesthetics: function default_aes: uneval draw_group: function draw_key: function draw_layer: function draw_panel: function extra_params: na.rm handle_na: function non_missing_aes: optional_aes: parameters: function required_aes: xmin ymin xmax ymax motif setup_data: function use_defaults: function super: <ggproto object: Class Geom, gg>

Examples


pcm <- read.table(file.path(find.package("motifStack"), 
                            "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")

df <- data.frame(xmin=c(.25, .25), ymin=c(.25, .75), xmax=c(.75, .75), ymax=c(.5, 1))
df$motif <- list(pcm2pfm(motif), pcm2pfm(motif))

library(ggplot2)

ggplot(df, aes(xmin=xmin, ymin=ymin, xmax=xmax, ymax=ymax, motif=motif)) + 
geom_motif() + theme_bw() + ylim(0, 1) + xlim(0, 1)


pcm <- read.table(file.path(find.package("motifStack"), 
                            "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")

df <- data.frame(xmin=c(.25, .25), ymin=c(.25, .75), xmax=c(.75, .75), ymax=c(.5, 1))
df$motif <- list(pcm2pfm(motif), pcm2pfm(motif))

library(ggplot2)

ggplot(df, aes(xmin=xmin, ymin=ymin, xmax=xmax, ymax=ymax, motif=motif)) + 
geom_motif() + theme_bw() + ylim(0, 1) + xlim(0, 1)

calculate ALLR from counts

Description

calculate ALLR from counts

Usage

getALLRscoreFromCounts(count1, count2, P1, P2, pseudo)
getALLRscoreFromCounts(count1, count2, P1, P2, pseudo)

Arguments

`count1`, `count2`	count in position j for matrix 1 or 2
`P1`, `P2`	background for matrix 1 or 2
`pseudo`	pseudocount

Value

numeric(1) of ALLR

Calculate distances between two profiles

Description

Calculate distances between two profiles

Usage

getDistance(hsp, count1, count2, P1, P2, pseudo)
getDistance(hsp, count1, count2, P1, P2, pseudo)

Arguments

`hsp`	output of traceBack function
`count1`, `count2`	motif profile 1 or 2
`P1`, `P2`	background of profile 1 or 2
`pseudo`	pseudocount

Value

full distance and aligned distance.

get the unique motif in each category grouped by distance

Description

to get the unique motif in a given category, eg by species.

Usage

getRankedUniqueMotifs(phylog, attr)
getRankedUniqueMotifs(phylog, attr)

Arguments

`phylog`	an object of class phylog
`attr`	attribute used for category of motifs

Value

return a list:

`uni.rank`	unique motif ranks
`uni.length`	length of unique motif grouped by distance
`uni.list`	unique motif names grouped by distance

Author(s)

Jianhong Ou

Examples


   if(interactive() || Sys.getenv("USER")=="jianhongou"){
        library("MotifDb")
        matrix.fly <- query(MotifDb, "Dmelanogaster")
        matrix.human <- query(MotifDb, "Hsapiens")
        pfms <- c(as.list(matrix.fly), as.list(matrix.human))
        pfms <- pfms[sample(seq_along(pfms), 100)]
        hc <- clusterMotifs(pfms)
        library(ade4)
        phylog <- ade4::hclust2phylog(hc)
        leaves <- names(phylog$leaves)
        attr <- gsub("^(.*?)_.*$", "\1", leaves)
        getRankedUniqueMotifs(phylog, attr)
    }

if(interactive() || Sys.getenv("USER")=="jianhongou"){
        library("MotifDb")
        matrix.fly <- query(MotifDb, "Dmelanogaster")
        matrix.human <- query(MotifDb, "Hsapiens")
        pfms <- c(as.list(matrix.fly), as.list(matrix.human))
        pfms <- pfms[sample(seq_along(pfms), 100)]
        hc <- clusterMotifs(pfms)
        library(ade4)
        phylog <- ade4::hclust2phylog(hc)
        leaves <- names(phylog$leaves)
        attr <- gsub("^(.*?)_.*$", "\1", leaves)
        getRankedUniqueMotifs(phylog, attr)
    }

Calculate pair_wise position score

Description

Calculate pair_wise position score

Usage

getScore(pcm1, pcm2, pseudo = 1)
getScore(pcm1, pcm2, pseudo = 1)

Arguments

`pcm1`, `pcm2`	object of pcm
`pseudo`	pseudocount

Value

A score matrix with nrow of ncol of pcm1 and ncol of ncol of pcm2.

add alpha transparency value to a color

Description

An alpha transparency value can be specified to a color, in order to get better color for background.

Usage

highlightCol(col, alpha = 0.5)
highlightCol(col, alpha = 0.5)

Arguments

`col`	vector of any of the three kinds of R color specifications, i.e., either a color name (as listed by colors()), a hexadecimal string of the form "#rrggbb" or "#rrggbbaa" (see rgb), or a positive integer i meaning palette()[i].
`alpha`	a value in [0, 1]

Value

a vector of colors in hexadecimal string of the form "#rrggbbaa".

Author(s)

Jianhong Ou

Examples


    highlightCol(1:5, 0.3)
    highlightCol(c("red", "green", "blue"), 0.3)

highlightCol(1:5, 0.3)
    highlightCol(c("red", "green", "blue"), 0.3)

import motifs from local files

Description

Import the motifs into pcm-class or pfm-class from files exported from Transfac, CisBP, and JASPAR.

Usage

importMatrix(
  filenames,
  format = c("auto", "pfm", "cm", "pcm", "meme", "transfac", "jaspar", "scpd", "cisbp",
    "psam", "xmatrix"),
  to = c("auto", "pcm", "pfm", "pssm", "psam")
)
importMatrix(
  filenames,
  format = c("auto", "pfm", "cm", "pcm", "meme", "transfac", "jaspar", "scpd", "cisbp",
    "psam", "xmatrix"),
  to = c("auto", "pcm", "pfm", "pssm", "psam")
)

Arguments

`filenames`	filename, an XMatrixList object, or an XMatrix object to be imported.
`format`	file format
`to`	import to pcm-class or pfm-class

Value

a list of object pcm-class or pfm-class

Author(s)

Jianhong Ou

Examples


  path <- system.file("extdata", package = "motifStack")
  importMatrix(dir(path, "*.pcm", full.names = TRUE))

path <- system.file("extdata", package = "motifStack")
  importMatrix(dir(path, "*.pcm", full.names = TRUE))

Class `marker`

Description

An object of class "marker" represents a marker in a motif

Usage

## S4 method for signature 'marker'
x$name
## S4 method for signature 'marker'
x$name

Arguments

`x`	A marker object
`name`	slot name of marker object

Objects from the Class

Objects can be created by calls of the form new("marker", type, start, stop, label, gp).

Examples


 new("marker", type="rect", start=c(2, 4), gp=gpar(lty=3))

new("marker", type="rect", start=c(2, 4), gp=gpar(lty=3))

Matrix Aligner

Description

Matrix Aligner is modified from Matalign-v4a. Matalign-v4a is a program to compare two positional specific matrices. The author of Matalign-v4a is Ting Wang and Gary Stormo.

Usage

matalign(
  pcms,
  method = c("Smith-Waterman", "Needleman-Wunsch"),
  pseudo = 1,
  revcomp = TRUE,
  ...
)
matalign(
  pcms,
  method = c("Smith-Waterman", "Needleman-Wunsch"),
  pseudo = 1,
  revcomp = TRUE,
  ...
)

Arguments

`pcms`	A list of pcm
`method`	Alignment method. "Smith-Waterman" or "Needleman-Wunsch". Default is "Smith-Waterma"
`pseudo`	pseudocount
`revcomp`	Check reverseComplement or not.
`...`	Not use.

Value

A data frame with alignment information. The column names are motif1, motif2, alignmentScore, startPos1, startPos2, endPos1, endPos2, alignmentLength.

Examples

if(interactive() || Sys.getenv("USER")=="jianhongou"){
  fp <- system.file("extdata", package="motifStack")
  fs <- dir(fp, "pcm$")
  pcms <- importMatrix(file.path(fp, fs), format="pcm")
  matalign(pcms)
 }
if(interactive() || Sys.getenv("USER")=="jianhongou"){
  fp <- system.file("extdata", package="motifStack")
  fs <- dir(fp, "pcm$")
  pcms <- importMatrix(file.path(fp, fs), format="pcm")
  matalign(pcms)
 }

merge multiple motifs

Description

merge multiple motifs by calculate mean of each position

Usage

mergeMotifs(..., bgNoise = NA)
mergeMotifs(..., bgNoise = NA)

Arguments

`...`	pcm or pfm objects
`bgNoise`	if it is not NA, test will using a background by Dirichlet(1)-distributed random frequencies with weight bg.noise. The value of bgNoise should be a number in the range of 0 to 1, eg. 0.05

Value

a pfm object

Author(s)

Jianhong Ou

Examples


    pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
    mergeMotifs(pcms)

pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
    mergeMotifs(pcms)

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

Description

plot sequence logo stacks with a radial phylogenic tree and multiple color rings. The difference from plotMotifStackWithRadialPhylog is that it has more color setting and one more group of pfms.

Usage

motifCircos(
  phylog,
  pfms = NULL,
  pfms2 = NULL,
  R = 2.5,
  r.tree = 1,
  col.tree.bg = NULL,
  col.tree.bg.alpha = 1,
  cnodes = 0,
  labels.nodes = names(phylog$nodes),
  clabel.nodes = 0,
  r.leaves = NA,
  cleaves = 1,
  labels.leaves = names(phylog$leaves),
  clabel.leaves = 1,
  col.leaves = rep("black", length(labels.leaves)),
  col.leaves.bg = NULL,
  col.leaves.bg.alpha = 1,
  r.pfms = NA,
  r.pfms2 = NA,
  r.rings = 0,
  col.rings = list(),
  col.inner.label.circle = NULL,
  inner.label.circle.width = 0.02,
  col.outer.label.circle = NULL,
  outer.label.circle.width = 0.02,
  draw.box = FALSE,
  clockwise = FALSE,
  init.angle = if (clockwise) 90 else 0,
  angle = 360,
  pfmNameSpliter = ";",
  rcpostfix = "(RC)",
  motifScale = c("linear", "logarithmic", "none"),
  ic.scale = TRUE,
  plotIndex = FALSE,
  IndexCol = "black",
  IndexCex = 0.8,
  groupDistance = NA,
  groupDistanceLineCol = "red",
  plotAxis = FALSE
)
motifCircos(
  phylog,
  pfms = NULL,
  pfms2 = NULL,
  R = 2.5,
  r.tree = 1,
  col.tree.bg = NULL,
  col.tree.bg.alpha = 1,
  cnodes = 0,
  labels.nodes = names(phylog$nodes),
  clabel.nodes = 0,
  r.leaves = NA,
  cleaves = 1,
  labels.leaves = names(phylog$leaves),
  clabel.leaves = 1,
  col.leaves = rep("black", length(labels.leaves)),
  col.leaves.bg = NULL,
  col.leaves.bg.alpha = 1,
  r.pfms = NA,
  r.pfms2 = NA,
  r.rings = 0,
  col.rings = list(),
  col.inner.label.circle = NULL,
  inner.label.circle.width = 0.02,
  col.outer.label.circle = NULL,
  outer.label.circle.width = 0.02,
  draw.box = FALSE,
  clockwise = FALSE,
  init.angle = if (clockwise) 90 else 0,
  angle = 360,
  pfmNameSpliter = ";",
  rcpostfix = "(RC)",
  motifScale = c("linear", "logarithmic", "none"),
  ic.scale = TRUE,
  plotIndex = FALSE,
  IndexCol = "black",
  IndexCex = 0.8,
  groupDistance = NA,
  groupDistanceLineCol = "red",
  plotAxis = FALSE
)

Arguments

`phylog`	an object of class phylog
`pfms`	a list of objects of class pfm
`pfms2`	a list of objects of class pfm
`R`	radius of canvas
`r.tree`	half width of the tree
`col.tree.bg`	a vector of colors for tree background
`col.tree.bg.alpha`	a alpha value [0, 1] of colors for tree background
`cnodes`	a character size for plotting the points that represent the nodes, used with par("cex")*cnodes. If zero, no points are drawn
`labels.nodes`	a vector of strings of characters for the nodes labels
`clabel.nodes`	a character size for the nodes labels, used with par("cex")*clabel.nodes. If zero, no nodes labels are drawn
`r.leaves`	width of the leaves
`cleaves`	a character size for plotting the points that represent the leaves, used with par("cex")*cleaves. If zero, no points are drawn
`labels.leaves`	a vector of strings of characters for the leaves labels
`clabel.leaves`	a character size for the leaves labels, used with par("cex")*clavel.leaves
`col.leaves`	a vector of colors for leaves labels
`col.leaves.bg`	a vector of colors for background of leaves labels
`col.leaves.bg.alpha`	alpha value [0, 1] for the colors of backgroud of leaves labels
`r.pfms`	width of the pfms
`r.pfms2`	width of the pfms2
`r.rings`	a vector of width of color rings
`col.rings`	a list of color rings
`col.inner.label.circle`	a vector of colors for inner cirlce of pfms
`inner.label.circle.width`	width for inner circle of pfms
`col.outer.label.circle`	a vector of colors for outer circle of pfms
`outer.label.circle.width`	width for outer circle of pfms
`draw.box`	if TRUE draws a box around the current plot with the function box()
`clockwise`	a logical value indicating if slices are drawn clockwise or counter clockwise
`init.angle`	number specifying the starting angle (in degrees) for the slices. Defaults to 0 (i.e., ‘3 o’clock') unless clockwise is true where init.angle defaults to 90 (degrees), (i.e., ‘12 o’clock')
`angle`	number specifying the angle (in degrees) for phylogenic tree. Defaults 360
`pfmNameSpliter`	spliter when name of pfms/pfms2 contain multiple node of labels.leaves
`rcpostfix`	the postfix for reverse complements
`motifScale`	the scale of logo size
`ic.scale`	logical. If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
`plotIndex`	logical. If TRUE, will plot index number in the motifLogo which can help user to describe the motifLogo
`IndexCol`	The color of the index number when plotIndex is TRUE.
`IndexCex`	The cex of the index number when plotIndex is TRUE.
`groupDistance`	show groupDistance on the draw
`groupDistanceLineCol`	groupDistance line color, default: red
`plotAxis`	logical. If TRUE, will plot distance axis.

Value

none

Author(s)

Jianhong Ou

Examples


if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                            names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
    library(RColorBrewer)
    color <- brewer.pal(12, "Set3")
    motifCircos(phylog, pfms, cleaves = 0.5, clabel.leaves = 0.7, 
                     col.tree.bg=rep(color, each=5), 
                     col.leaves=rep(color, each=5),
                      r.rings=c(0.02, 0.03, 0.04), 
                      col.rings=list(sample(colors(), 50), 
                                     sample(colors(), 50), 
                                     sample(colors(), 50)))
  }

if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                            names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
    library(RColorBrewer)
    color <- brewer.pal(12, "Set3")
    motifCircos(phylog, pfms, cleaves = 0.5, clabel.leaves = 0.7, 
                     col.tree.bg=rep(color, each=5), 
                     col.leaves=rep(color, each=5),
                      r.rings=c(0.02, 0.03, 0.04), 
                      col.rings=list(sample(colors(), 50), 
                                     sample(colors(), 50), 
                                     sample(colors(), 50)))
  }

plot a DNA sequence logo cloud

Description

Plot a DNA sequence logo cloud

Usage

motifCloud(
  motifSig,
  rcpostfix = "(RC)",
  layout = c("rectangles", "cloud", "tree"),
  scale = c(6, 0.5),
  rot.per = 0.1,
  draw.box = TRUE,
  draw.freq = TRUE,
  box.col = "gray",
  freq.col = "gray",
  group.col = NULL,
  groups = NULL,
  draw.legend = FALSE,
  font = "sans",
  ic.scale = TRUE
)
motifCloud(
  motifSig,
  rcpostfix = "(RC)",
  layout = c("rectangles", "cloud", "tree"),
  scale = c(6, 0.5),
  rot.per = 0.1,
  draw.box = TRUE,
  draw.freq = TRUE,
  box.col = "gray",
  freq.col = "gray",
  group.col = NULL,
  groups = NULL,
  draw.legend = FALSE,
  font = "sans",
  ic.scale = TRUE
)

Arguments

`motifSig`	an object of class motifSig
`rcpostfix`	postfix for reverse-complement motif names, default: (RC)
`layout`	layout of the logo cloud, rectangles, cloud or tree
`scale`	A vector of length 2 indicating the range of the size of the sequence logo.
`rot.per`	proportion sequence logo with 90 degree rotation. Only work for "cloud" layout
`draw.box`	draw box for each sequence logo or not
`draw.freq`	label frequency of each signature or not
`box.col`	color of box for each sequence logo
`freq.col`	color of frequency label
`group.col`	color setting for groups
`groups`	a named vectors of motif groups
`draw.legend`	draw group color legend or not
`font`	font of logo
`ic.scale`	logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.

Value

none

Examples


  if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                            names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    motifSig <- motifSignature(pfms, phylog, cutoffPval=0.0001)
    motifCloud(motifSig)
  }

if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                            names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    motifSig <- motifSignature(pfms, phylog, cutoffPval=0.0001)
    motifCloud(motifSig)
  }

Motif Grob

Description

This function create a motif grob.

Usage

motifGrob(
  pfm,
  x = unit(0.5, "npc"),
  y = unit(0.5, "npc"),
  width = unit(1, "npc"),
  height = unit(1, "npc"),
  angle = 0,
  ic.scale = TRUE,
  default.units = "native",
  name = NULL,
  gp = gpar(fontfamily = "sans", fontface = "bold")
)
motifGrob(
  pfm,
  x = unit(0.5, "npc"),
  y = unit(0.5, "npc"),
  width = unit(1, "npc"),
  height = unit(1, "npc"),
  angle = 0,
  ic.scale = TRUE,
  default.units = "native",
  name = NULL,
  gp = gpar(fontfamily = "sans", fontface = "bold")
)

Arguments

`pfm`	an object of pfm
`x`	A numeric vector or unit object specifying x-values.
`y`	A numeric vector or unit object specifying y-values.
`width`	A numeric vector or unit object specifying width.
`height`	A numeric vector or unit object specifying height.
`angle`	A numeric value indicating the angle of rotation of the motif. Positive values indicate the amount of rotation, in degrees, anticlockwise from the positive x-axis.
`ic.scale`	logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
`default.units`	A string indicating the default units to use if x, y, width, or height are only given as numeric vectors.
`name`	A character value to uniquely identify the motifGrob once it has been pushed onto the grob tree.
`gp`	A gpar object, typically the output from a call to the function gpar. The list will be used as parameter of plotMotifLogoA.

Value

An gTree object.

Author(s)

Jianhong Ou

Examples


pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
pfm<-pcm2pfm(pcm)
rownames(pfm)<-c("A","C","G","T")
motif <- new("pfm", mat=pfm, name="bin_SOLEXA")
motifGrob(motif)

pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
pfm<-pcm2pfm(pcm)
rownames(pfm)<-c("A","C","G","T")
motif <- new("pfm", mat=pfm, name="bin_SOLEXA")
motifGrob(motif)

Hierarchical Clustering motifs

Description

functions to perfom clustering of output of matalign

Usage

motifHclust(align, ...)
motifHclust(align, ...)

Arguments

`align`	output of matalign, used to generate distance matrix.
`...`	parameter to pass to the hclust.

Value

An object of hclust.

Examples

 if(interactive() || Sys.getenv("USER")=="jianhongou"){
  fp <- system.file("extdata", package="motifStack")
  fs <- dir(fp, "pcm$")
  pcms <- importMatrix(file.path(fp, fs), format="pcm")
  align <- matalign(pcms)
  hc <- motifHclust(align, method="average")
 }
if(interactive() || Sys.getenv("USER")=="jianhongou"){
  fp <- system.file("extdata", package="motifStack")
  fs <- dir(fp, "pcm$")
  pcms <- importMatrix(file.path(fp, fs), format="pcm")
  align <- matalign(pcms)
  hc <- motifHclust(align, method="average")
 }

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

Description

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

Usage

motifPiles(
  phylog,
  pfms = NULL,
  pfms2 = NULL,
  r.tree = 0.45,
  col.tree = NULL,
  cnodes = 0,
  labels.nodes = names(phylog$nodes),
  clabel.nodes = 0,
  cleaves = 0.2,
  labels.leaves = names(phylog$leaves),
  clabel.leaves = 1,
  col.leaves = rep("black", length(labels.leaves)),
  col.leaves.bg = NULL,
  col.leaves.bg.alpha = 1,
  r.pfms = NA,
  r.pfms2 = NA,
  motifScale = c("logarithmic", "linear", "none"),
  col.pfms = NULL,
  col.pfms.width = 0.02,
  col.pfms2 = NULL,
  col.pfms2.width = 0.02,
  r.anno = 0,
  col.anno = list(),
  pfmNameSpliter = ";",
  rcpostfix = "(RC)",
  ic.scale = TRUE,
  plotIndex = FALSE,
  IndexCol = "black",
  IndexCex = 0.8,
  groupDistance = NA,
  groupDistanceLineCol = "red"
)
motifPiles(
  phylog,
  pfms = NULL,
  pfms2 = NULL,
  r.tree = 0.45,
  col.tree = NULL,
  cnodes = 0,
  labels.nodes = names(phylog$nodes),
  clabel.nodes = 0,
  cleaves = 0.2,
  labels.leaves = names(phylog$leaves),
  clabel.leaves = 1,
  col.leaves = rep("black", length(labels.leaves)),
  col.leaves.bg = NULL,
  col.leaves.bg.alpha = 1,
  r.pfms = NA,
  r.pfms2 = NA,
  motifScale = c("logarithmic", "linear", "none"),
  col.pfms = NULL,
  col.pfms.width = 0.02,
  col.pfms2 = NULL,
  col.pfms2.width = 0.02,
  r.anno = 0,
  col.anno = list(),
  pfmNameSpliter = ";",
  rcpostfix = "(RC)",
  ic.scale = TRUE,
  plotIndex = FALSE,
  IndexCol = "black",
  IndexCex = 0.8,
  groupDistance = NA,
  groupDistanceLineCol = "red"
)

Arguments

`phylog`	an object of class phylog
`pfms`	a list of objects of class pfm
`pfms2`	a list of objects of class pfm
`r.tree`	width of the tree
`col.tree`	a vector of colors for tree
`cnodes`	a character size for plotting the points that represent the nodes, used with par("cex")*cnodes. If zero, no points are drawn
`labels.nodes`	a vector of strings of characters for the nodes labels
`clabel.nodes`	a character size for the nodes labels, used with par("cex")*clabel.nodes. If zero, no nodes labels are drawn
`cleaves`	a character size for plotting the points that represent the leaves, used with par("cex")*cleaves. If zero, no points are drawn
`labels.leaves`	a vector of strings of characters for the leaves labels
`clabel.leaves`	a character size for the leaves labels, used with par("cex")*clavel.leaves
`col.leaves`	a vector of colors for leaves labels
`col.leaves.bg`	a vector of colors for background of leaves labels
`col.leaves.bg.alpha`	alpha value [0, 1] for the colors of backgroud of leaves labels
`r.pfms`	width of the pfms
`r.pfms2`	width of the pfms2
`motifScale`	the scale of logo size
`col.pfms`	a vector of colors for inner pile of pfms
`col.pfms.width`	width for inner pile of pfms
`col.pfms2`	a vector of colors for outer pile of pfms
`col.pfms2.width`	width for outer pile of pfms
`r.anno`	a vector of width of color sets
`col.anno`	a list of color sets
`pfmNameSpliter`	spliter when name of pfms/pfms2 contain multiple node of labels.leaves
`rcpostfix`	the postfix for reverse complements
`ic.scale`	logical. If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
`plotIndex`	logical. If TRUE, will plot index number in the motifLogo which can help user to describe the motifLogo
`IndexCol`	The color of the index number when plotIndex is TRUE.
`IndexCex`	The cex of the index number when plotIndex is TRUE.
`groupDistance`	show groupDistance on the draw
`groupDistanceLineCol`	groupDistance line color, default: red

Value

none

Author(s)

Jianhong Ou

Examples


if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                           names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
    library(RColorBrewer)
    color <- brewer.pal(12, "Set3")
    motifPiles(phylog, pfms, cleaves = 0.5, clabel.leaves = 0.7, 
             col.leaves=rep(color, each=5), 
             col.leaves.bg = sample(colors(), 50),
             col.tree=rep(color, each=5),
             r.anno=c(0.02, 0.03, 0.04), 
             col.anno=list(sample(colors(), 50), 
                            sample(colors(), 50), 
                            sample(colors(), 50)))
  }

if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                           names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
    library(RColorBrewer)
    color <- brewer.pal(12, "Set3")
    motifPiles(phylog, pfms, cleaves = 0.5, clabel.leaves = 0.7, 
             col.leaves=rep(color, each=5), 
             col.leaves.bg = sample(colors(), 50),
             col.tree=rep(color, each=5),
             r.anno=c(0.02, 0.03, 0.04), 
             col.anno=list(sample(colors(), 50), 
                            sample(colors(), 50), 
                            sample(colors(), 50)))
  }

Class `"motifSig"`

Description

An object of class "motifSig" represents the output of function motifSignature

methods for motifSig objects.

Usage

signatures(object)

frequence(object)

nodelist(object)

sigColor(object)

## S4 method for signature 'motifSig'
x$name
signatures(object)

frequence(object)

nodelist(object)

sigColor(object)

## S4 method for signature 'motifSig'
x$name

Arguments

`object`	An object of class `motifSig`.
`x`	A motifSig object
`name`	slot name of motifSig object

Objects from the Class

Objects can be created by calls of the form new("motifSig", signature, freq, nodelist, gpcol).

Methods

signatures: signature(object = "motifSig") return the signatures of motifSig
frequence: signature(object = "motifSig") return the frequency of motifSig
nodelist: signature(object = "motifSig") return the nodelist of motifSig
sigColor: signature(object = "motifSig") return the group color sets of motifSig
$, $<-: Get or set the slot of motifSig

get signatures from motifs

Description

extract signatures from multiple motifs by distance calculated from STAMP

Usage

motifSignature(
  pfms,
  phylog,
  cutoffPval,
  groupDistance,
  rcpostfix = "(RC)",
  min.freq = 2,
  trim = 0.2,
  families = list(),
  sort = TRUE
)
motifSignature(
  pfms,
  phylog,
  cutoffPval,
  groupDistance,
  rcpostfix = "(RC)",
  min.freq = 2,
  trim = 0.2,
  families = list(),
  sort = TRUE
)

Arguments

`pfms`	a list of objects of class pfm
`phylog`	an object of class phylog
`cutoffPval`	pvalue for motifs to merge.
`groupDistance`	maxmal distance of motifs in the same group
`rcpostfix`	postfix for reverse-complement motif names, default: (RC)
`min.freq`	signatures with frequency below min.freq will not be plotted
`trim`	minimal information content for each position of signature
`families`	for each family, the motif number in one signature should only count as 1
`sort`	sort the signatures by frequency or not.

Value

an Object of class motifSig

Examples


  if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                            names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    motifSig <- motifSignature(pfms, phylog, cutoffPval=0.0001)
  }

if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                            names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    motifSig <- motifSignature(pfms, phylog, cutoffPval=0.0001)
  }

plot a DNA sequence logo stack

Description

Plot a DNA sequence logo stack

Usage

motifStack(
  pfms,
  layout = c("stack", "treeview", "phylog", "radialPhylog"),
  reorder = TRUE,
  ...
)
motifStack(
  pfms,
  layout = c("stack", "treeview", "phylog", "radialPhylog"),
  reorder = TRUE,
  ...
)

Arguments

`pfms`	a list of objects of class pfm
`layout`	layout of the logo stack, stack, treeview or radialPhylog
`reorder`	logical(1). Default TRUE. Set to FALSE will do alignment but keep the order of the pfms. This parameter only work for stack layout.
`...`	any parameters could to pass to plotMotifLogoStack, plotMotifLogoStackWithTree, plotMotifStackWithPhylog or plotMotifStackWithRadialPhylog. And the 'revcomp' parameter for DNAmotifAlignment.

Value

return a list contains pfms and phylog

Examples


  if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                            names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    motifStack(pfms, "radialPhylog")
    
    ## AA motifs
    pcms<-importMatrix(system.file("extdata", "prot.meme", 
                                   package="motifStack"),
                   format="meme", to="pfm")
    motifStack(pcms[1:5])
    motifStack(pcms[1:5], reorder=FALSE)
  }

if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                            names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    motifStack(pfms, "radialPhylog")
    
    ## AA motifs
    pcms<-importMatrix(system.file("extdata", "prot.meme", 
                                   package="motifStack"),
                   format="meme", to="pfm")
    motifStack(pcms[1:5])
    motifStack(pcms[1:5], reorder=FALSE)
  }

Class `ouNode`

Description

An object of class "ouNode" represents a motif node in a cluster tree

Usage

## S4 method for signature 'ouNode'
x$name
## S4 method for signature 'ouNode'
x$name

Arguments

`x`	A ouNode object
`name`	slot name of ouNode object

Objects from the Class

Objects can be created by calls of the form new("ouNode", left, right, parent, distl, distr, sizel, sizer).

Examples


 new("ouNode", left="A", right="B", parent="Root", distl=1, distr=2, sizel=1, sizer=1)

new("ouNode", left="A", right="B", parent="Root", distl=1, distr=2, sizel=1, sizer=1)

Class `"pcm"`

Description

An object of class "pcm" represents the position count matrix of a DNA/RNA/amino-acid sequence motif. The entry stores a matrix, which in row i, column j gives the counts of observing nucleotide/or amino acid i in position j of the motif.

methods for pcm objects.

Usage

## S4 method for signature 'pcm'
x$name

## S4 method for signature 'pcm,ANY'
plot(x, y = "missing", ...)

trimMotif(x, t)

matrixReverseComplement(x)

addBlank(x, n, b)

getIC(x, p)

pcm2pfm(x, background)

pcm2pssm(x, background)

## S4 method for signature 'pcm'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'pcm'
format(x, ...)
## S4 method for signature 'pcm'
x$name

## S4 method for signature 'pcm,ANY'
plot(x, y = "missing", ...)

trimMotif(x, t)

matrixReverseComplement(x)

addBlank(x, n, b)

getIC(x, p)

pcm2pfm(x, background)

pcm2pssm(x, background)

## S4 method for signature 'pcm'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'pcm'
format(x, ...)

Arguments

`x`	An object of class `pcm`. For `getIC`, if parameter p is followed, x should be an object of matrix. For `pcm2pfm`, x also could be an object of matrix.
`name`	slot name of pcm object.
`y`	Not use.
`...`	Further potential arguments passed to `plotMotifLogo`.
`t`	numeric value of information content threshold for trimming.
`n`	how many spaces should be added.
`b`	logical value to indicate where the space should be added.
`p`	p is the background frequency.
`background`	a `"numeric"` vector. The background frequency.
`row.names`, `optional`	see as.data.frame

Objects from the Class

Objects can be created by calls of the form new("pcm", mat, name, alphabet, color, background).

Methods

addBlank: signature(x="pcm", n="numeric", b="logical") add space into the position count matrix for alignment. b is a bool value, if TRUE, add space to the 3' end, else add space to the 5' end. n indicates how many spaces should be added.
coerce: signature(from = "pcm", to = "matrix"): convert object pcm to matrix
getIC: signature(x = "pcm",) Calculate information content profile for position frequency matrix.
matrixReverseComplement: signature(x = "pcm") get the reverse complement of position frequency matrix.
plot: signature(x = "pcm") Plots the sequence logo of the position count matrix.
trimMotif: signature(x = "pcm", t= "numeric") trim motif by information content.
$, $<-: Get or set the slot of pcm-class
as.data.frame: convert pcm-class to a data.frame
format: return the name_pcm of pcm-class

Examples


pcm <- read.table(file.path(find.package("motifStack"), "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")
plot(motif)
pcm2pfm(pcm)
pcm2pssm(pcm)

pcm <- read.table(file.path(find.package("motifStack"), "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")
getIC(motif)
matrixReverseComplement(motif)
as(motif,"matrix")
pcm2pfm(motif)
as.data.frame(motif)
format(motif)

pcm <- read.table(file.path(find.package("motifStack"), "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")
plot(motif)
pcm2pfm(pcm)
pcm2pssm(pcm)

pcm <- read.table(file.path(find.package("motifStack"), "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")
getIC(motif)
matrixReverseComplement(motif)
as(motif,"matrix")
pcm2pfm(motif)
as.data.frame(motif)
format(motif)

Class `"pfm"`

Description

An object of class "pfm" represents the position frequency matrix of a DNA/RNA/amino-acid sequence motif. The entry stores a matrix, which in row i, column j gives the frequency of observing nucleotide/or amino acid i in position j of the motif.

methods for pfm objects.

Usage

## S4 method for signature 'pfm'
x$name

## S4 method for signature 'pfm,ANY'
plot(x, y = "missing", ...)

## S4 method for signature 'pfm,ANY'
getIC(x, p = "missing")

## S4 method for signature 'pfm,numeric'
trimMotif(x, t)

## S4 method for signature 'pfm'
matrixReverseComplement(x)

## S4 method for signature 'pfm,numeric,logical'
addBlank(x, n, b)

## S4 method for signature 'pfm'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'pfm'
format(x, ...)
## S4 method for signature 'pfm'
x$name

## S4 method for signature 'pfm,ANY'
plot(x, y = "missing", ...)

## S4 method for signature 'pfm,ANY'
getIC(x, p = "missing")

## S4 method for signature 'pfm,numeric'
trimMotif(x, t)

## S4 method for signature 'pfm'
matrixReverseComplement(x)

## S4 method for signature 'pfm,numeric,logical'
addBlank(x, n, b)

## S4 method for signature 'pfm'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'pfm'
format(x, ...)

Arguments

`x`	An object of class `pfm`. For `getIC`, if parameter p is followed, x should be an object of matrix.
`name`	Slot name.
`y`	Not use.
`...`	Further potential arguments passed to `plotMotifLogo`.
`p`	p is the background frequency.
`t`	numeric value of information content threshold for trimming.
`n`	how many spaces should be added.
`b`	logical value to indicate where the space should be added.
`row.names`, `optional`	see as.data.frame

Objects from the Class

Objects can be created by calls of the form new("pfm", mat, name, alphabet, color, background).

Methods

addBlank: signature(x="pfm", n="numeric", b="logical") add space into the position frequency matrix for alignment. b is a bool value, if TRUE, add space to the 3' end, else add space to the 5' end. n indicates how many spaces should be added.
getIC: signature(x = "pfm",) Calculate information content profile for position frequency matrix.
getIC: signature(x = "matrix", p = "numeric") Calculate information content profile for matrix. p is the background frequency
matrixReverseComplement: signature(x = "pfm") get the reverse complement of position frequency matrix.
plot: signature(x = "pfm") Plots the sequence logo of the position frequency matrix.
trimMotif: signature(x = "pfm", t= "numeric") trim motif by information content.
$, $<-: Get or set the slot of pfm-class
as.data.frame: convert pfm-class to a data.frame
format: return the name_pfm of pfm-class

Examples


pcm <- read.table(file.path(find.package("motifStack"), "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- pcm2pfm(pcm)
motif <- new("pfm", mat=motif, name="bin_SOLEXA")
plot(motif)


pcm <- read.table(file.path(find.package("motifStack"), "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- pcm2pfm(pcm)
motif <- new("pfm", mat=motif, name="bin_SOLEXA")
getIC(motif)
matrixReverseComplement(motif)
addBlank(motif, 1, FALSE)
addBlank(motif, 3, TRUE)
as(motif,"matrix")
as.data.frame(motif)
format(motif)

pcm <- read.table(file.path(find.package("motifStack"), "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- pcm2pfm(pcm)
motif <- new("pfm", mat=motif, name="bin_SOLEXA")
plot(motif)


pcm <- read.table(file.path(find.package("motifStack"), "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- pcm2pfm(pcm)
motif <- new("pfm", mat=motif, name="bin_SOLEXA")
getIC(motif)
matrixReverseComplement(motif)
addBlank(motif, 1, FALSE)
addBlank(motif, 3, TRUE)
as(motif,"matrix")
as.data.frame(motif)
format(motif)

convert pfm object to PWM

Description

convert pfm object to PWM

Usage

pfm2pwm(x, N = 10000)
pfm2pwm(x, N = 10000)

Arguments

`x`	an object of `pfm` or `pcm` or matrix
`N`	Total number of event counts used for pfm generation.

Value

A numeric matrix representing the Position Weight Matrix for PWM.

Author(s)

Jianhong Ou

Examples


library("MotifDb")
matrix.fly <- query(MotifDb, "Dmelanogaster")
pfm2pwm(matrix.fly[[1]])

library("MotifDb")
matrix.fly <- query(MotifDb, "Dmelanogaster")
pfm2pwm(matrix.fly[[1]])

plot affinity logo

Description

plot affinity logo

Usage

plotAffinityLogo(
  psam,
  motifName,
  font = "sans",
  fontface = "bold",
  colset = c("#00811B", "#2000C7", "#FFB32C", "#D00001"),
  alpha = 0.5,
  newpage = TRUE,
  draw = TRUE
)
plotAffinityLogo(
  psam,
  motifName,
  font = "sans",
  fontface = "bold",
  colset = c("#00811B", "#2000C7", "#FFB32C", "#D00001"),
  alpha = 0.5,
  newpage = TRUE,
  draw = TRUE
)

Arguments

`psam`	a position-specific affinity matrix
`motifName`	motif name
`font`	font of logo
`fontface`	fontface of logo
`colset`	color setting for each logo letter
`alpha`	Alpha channel for transparency of low affinity letters.
`newpage`	plot in a new canvas or not.
`draw`	Vector (logical(1)). TRUE to plot. FALSE, return a gList

Value

none

References

Barrett C. Foat, Alexandre V. Morozov, Harmen J. Bussemaker; Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE, Bioinformatics, Volume 22, Issue 14, 15 July 2006, Pages e141-e149, https://doi.org/10.1093/bioinformatics/btl223

Examples


psam <- importMatrix(file.path(find.package("motifStack"), "extdata", "PSAM.mxr"), 
                     format="psam")[[1]]
plotAffinityLogo(psam)

psam <- importMatrix(file.path(find.package("motifStack"), "extdata", "PSAM.mxr"), 
                     format="psam")[[1]]
plotAffinityLogo(psam)

plot sequence logo

Description

plot amino acid or DNA sequence logo

Usage

plotMotifLogo(
  pfm,
  motifName,
  p = rep(0.25, 4),
  font = "sans",
  fontface = "bold",
  colset = c("#00811B", "#2000C7", "#FFB32C", "#D00001"),
  xaxis = TRUE,
  yaxis = TRUE,
  xlab = "position",
  ylab = "bits",
  xlcex = 1.2,
  ylcex = 1.2,
  ncex = 1.2,
  ic.scale = TRUE,
  newpage = TRUE,
  margins = c(4.1, 4.1, 2.1, 0.1),
  draw = TRUE,
  ...
)
plotMotifLogo(
  pfm,
  motifName,
  p = rep(0.25, 4),
  font = "sans",
  fontface = "bold",
  colset = c("#00811B", "#2000C7", "#FFB32C", "#D00001"),
  xaxis = TRUE,
  yaxis = TRUE,
  xlab = "position",
  ylab = "bits",
  xlcex = 1.2,
  ylcex = 1.2,
  ncex = 1.2,
  ic.scale = TRUE,
  newpage = TRUE,
  margins = c(4.1, 4.1, 2.1, 0.1),
  draw = TRUE,
  ...
)

Arguments

`pfm`	a position frequency matrices
`motifName`	motif name
`p`	background possibility
`font`	font of logo
`fontface`	fontface of logo
`colset`	color setting for each logo letter
`xaxis`	draw x-axis or not. If a vector of character or numeric is provided, the function will try to plot the x-axis by setting the labels as the vectors.
`yaxis`	draw y-axis or not
`xlab`	x-label, do nothing if set xlab as NA
`ylab`	y-label, do nothing if set ylab as NA
`xlcex`	cex value for x-label
`ylcex`	cex value for y-label
`ncex`	cex value for motif name
`ic.scale`	logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height. It will also can be set as FALSE followed by a numeric vectors. The format is c(FALSE, scale). If it is FALSE followed by a number (eg c(FALSE, 100)), the y axis labels will be re-scaled by 100.
`newpage`	logical If TRUE, plot it in a new page.
`margins`	A numeric vector interpreted in the same way as par(mar) in base graphics.
`draw`	Vector (logical(1)). TRUE to plot. FALSE, return a gList
`...`	Not used.

Value

none

Examples


pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
pfm<-pcm2pfm(pcm)
rownames(pfm)<-c("A","C","G","T")
plotMotifLogo(pfm)

pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
pfm<-pcm2pfm(pcm)
rownames(pfm)<-c("A","C","G","T")
plotMotifLogo(pfm)

plot sequence logo without plot.new

Description

plot amino acid or DNA sequence logo in a given canvas

Usage

plotMotifLogoA(
  pfm,
  font = "sans",
  fontface = "bold",
  ic.scale = TRUE,
  draw = TRUE
)
plotMotifLogoA(
  pfm,
  font = "sans",
  fontface = "bold",
  ic.scale = TRUE,
  draw = TRUE
)

Arguments

`pfm`	an object of pfm
`font`	font of logo
`fontface`	fontface of logo
`ic.scale`	logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
`draw`	Vector (logical(1)). TRUE to plot. FALSE, return a gList

Value

none

Examples


pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
pfm<-pcm2pfm(pcm)
rownames(pfm)<-c("A","C","G","T")
motif <- new("pfm", mat=pfm, name="bin_SOLEXA")
plotMotifLogoA(motif)

pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
pfm<-pcm2pfm(pcm)
rownames(pfm)<-c("A","C","G","T")
motif <- new("pfm", mat=pfm, name="bin_SOLEXA")
plotMotifLogoA(motif)

plot sequence logos stack

Description

plot sequence logos stack

Usage

plotMotifLogoStack(pfms, ...)
plotMotifLogoStack(pfms, ...)

Arguments

`pfms`	a list of position frequency matrices, pfms must be a list of class pfm
`...`	other parameters can be passed to plotMotifLogo function

Value

none

Examples


  pcm1<-matrix(c(0,50,0,50,
           100,0,0,0,
           0,100,0,0,
           0,0,100,0,
           0,0,0,100,
           50,50,0,0,
           0,0,50,50), nrow=4)
  pcm2<-matrix(c(50,50,0,0,
           0,100,0,0,
           0,50,50,0,
           0,0,0,100,
           50,50,0,0,
           0,0,50,50), nrow=4)
  rownames(pcm1)<-c("A","C","G","T")
  rownames(pcm2)<-c("A","C","G","T")
  pfms<-list(p1=new("pfm",mat=pcm2pfm(pcm1),name="m1"),
         p2=new("pfm",mat=pcm2pfm(pcm2),name="m2"))
  pfms<-DNAmotifAlignment(pfms)
  plotMotifLogoStack(pfms)

pcm1<-matrix(c(0,50,0,50,
           100,0,0,0,
           0,100,0,0,
           0,0,100,0,
           0,0,0,100,
           50,50,0,0,
           0,0,50,50), nrow=4)
  pcm2<-matrix(c(50,50,0,0,
           0,100,0,0,
           0,50,50,0,
           0,0,0,100,
           50,50,0,0,
           0,0,50,50), nrow=4)
  rownames(pcm1)<-c("A","C","G","T")
  rownames(pcm2)<-c("A","C","G","T")
  pfms<-list(p1=new("pfm",mat=pcm2pfm(pcm1),name="m1"),
         p2=new("pfm",mat=pcm2pfm(pcm2),name="m2"))
  pfms<-DNAmotifAlignment(pfms)
  plotMotifLogoStack(pfms)

plot sequence logos stack with hierarchical cluster tree

Description

plot sequence logos stack with hierarchical cluster tree

Usage

plotMotifLogoStackWithTree(pfms, hc, treewidth = 1/8, trueDist = FALSE, ...)
plotMotifLogoStackWithTree(pfms, hc, treewidth = 1/8, trueDist = FALSE, ...)

Arguments

`pfms`	a list of position frequency matrices, pfms must be a list of class pfm
`hc`	an object of the type produced by stats::hclust
`treewidth`	the width to show tree
`trueDist`	logical flags to use hclust height or not.
`...`	other parameters can be passed to plotMotifLogo function

Value

none

Examples


  #####Input#####
  pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")

  #####Clustering#####
  hc <- clusterMotifs(pcms)

  ##reorder the motifs for plotMotifLogoStack
  motifs<-pcms[hc$order]
  motifs <- lapply(motifs, pcm2pfm)
  ##do alignment
  motifs<-DNAmotifAlignment(motifs)
  ##plot stacks
  plotMotifLogoStack(motifs, ncex=1.0)
  plotMotifLogoStackWithTree(motifs, hc=hc)

#####Input#####
  pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")

  #####Clustering#####
  hc <- clusterMotifs(pcms)

  ##reorder the motifs for plotMotifLogoStack
  motifs<-pcms[hc$order]
  motifs <- lapply(motifs, pcm2pfm)
  ##do alignment
  motifs<-DNAmotifAlignment(motifs)
  ##plot stacks
  plotMotifLogoStack(motifs, ncex=1.0)
  plotMotifLogoStackWithTree(motifs, hc=hc)

plot motif over another motif

Description

plot motif over another motif to emphesize the difference.

Usage

plotMotifOverMotif(
  motif,
  backgroundMotif,
  bgNoise = NA,
  font = "sans",
  textgp = gpar()
)
plotMotifOverMotif(
  motif,
  backgroundMotif,
  bgNoise = NA,
  font = "sans",
  textgp = gpar()
)

Arguments

`motif`	an object of `pcm` or `pfm`
`backgroundMotif`	an object of `pcm` or `pfm`
`bgNoise`	if it is not NA, test will using a background by Dirichlet(1)-distributed random frequencies with weight bg.noise. The value of bgNoise should be a number in the range of 0 to 1, eg. 0.05
`font`	font for logo symbol
`textgp`	text parameter

Value

none

Examples


pcms <- readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
len <- sapply(pcms, function(.ele) ncol(.ele$mat))
pcms <- pcms[len==7]
plotMotifOverMotif(pcms[[1]], pcms[[2]], bgNoise=0.05)

pcms <- readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
len <- sapply(pcms, function(.ele) ncol(.ele$mat))
pcms <- pcms[len==7]
plotMotifOverMotif(pcms[[1]], pcms[[2]], bgNoise=0.05)

plot sequence logo stacks with a ape4-style phylogenic tree

Description

plot sequence logo stacks with a ape4-style phylogenic tree

Usage

plotMotifStackWithPhylog(
  phylog,
  pfms = NULL,
  f.phylog = 0.3,
  f.logo = NULL,
  cleaves = 1,
  cnodes = 0,
  labels.leaves = names(phylog$leaves),
  clabel.leaves = 1,
  labels.nodes = names(phylog$nodes),
  clabel.nodes = 0,
  font = "sans",
  ic.scale = TRUE,
  ...
)
plotMotifStackWithPhylog(
  phylog,
  pfms = NULL,
  f.phylog = 0.3,
  f.logo = NULL,
  cleaves = 1,
  cnodes = 0,
  labels.leaves = names(phylog$leaves),
  clabel.leaves = 1,
  labels.nodes = names(phylog$nodes),
  clabel.nodes = 0,
  font = "sans",
  ic.scale = TRUE,
  ...
)

Arguments

`phylog`	an object of class phylog
`pfms`	a list of objects of class pfm
`f.phylog`	a size coefficient for tree size (a parameter to draw the tree in proportion to leaves label)
`f.logo`	a size coefficient for the motif
`cleaves`	a character size for plotting the points that represent the leaves, used with par("cex")*cleaves. If zero, no points are drawn
`cnodes`	a character size for plotting the points that represent the nodes, used with par("cex")*cnodes. If zero, no points are drawn
`labels.leaves`	a vector of strings of characters for the leaves labels
`clabel.leaves`	a character size for the leaves labels, used with par("cex")*clavel.leaves
`labels.nodes`	a vector of strings of characters for the nodes labels
`clabel.nodes`	a character size for the nodes labels, used with par("cex")*clabel.nodes. If zero, no nodes labels are drawn
`font`	font of logo
`ic.scale`	logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
`...`	not used.

Value

none

Examples


  if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
    plotMotifStackWithPhylog(phylog, pfms, f.phylog=0.3, 
                             cleaves = 0.5, clabel.leaves = 0.7)
  }

if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
    plotMotifStackWithPhylog(phylog, pfms, f.phylog=0.3, 
                             cleaves = 0.5, clabel.leaves = 0.7)
  }

plot sequence logo stacks with a radial phylogenic tree

Description

plot sequence logo stacks with a radial phylogenic tree

Usage

plotMotifStackWithRadialPhylog(
  phylog,
  pfms = NULL,
  circle = 0.75,
  circle.motif = NA,
  cleaves = 1,
  cnodes = 0,
  labels.leaves = names(phylog$leaves),
  clabel.leaves = 1,
  labels.nodes = names(phylog$nodes),
  clabel.nodes = 0,
  draw.box = FALSE,
  col.leaves = rep("black", length(labels.leaves)),
  col.leaves.bg = NULL,
  col.leaves.bg.alpha = 1,
  col.bg = NULL,
  col.bg.alpha = 1,
  col.inner.label.circle = NULL,
  inner.label.circle.width = "default",
  col.outer.label.circle = NULL,
  outer.label.circle.width = "default",
  clockwise = FALSE,
  init.angle = if (clockwise) 90 else 0,
  angle = 360,
  pfmNameSpliter = ";",
  rcpostfix = "(RC)",
  motifScale = c("linear", "logarithmic"),
  ic.scale = TRUE,
  plotIndex = FALSE,
  IndexCol = "black",
  IndexCex = 0.8,
  groupDistance = NA,
  groupDistanceLineCol = "red",
  plotAxis = FALSE,
  font = "sans",
  ...
)
plotMotifStackWithRadialPhylog(
  phylog,
  pfms = NULL,
  circle = 0.75,
  circle.motif = NA,
  cleaves = 1,
  cnodes = 0,
  labels.leaves = names(phylog$leaves),
  clabel.leaves = 1,
  labels.nodes = names(phylog$nodes),
  clabel.nodes = 0,
  draw.box = FALSE,
  col.leaves = rep("black", length(labels.leaves)),
  col.leaves.bg = NULL,
  col.leaves.bg.alpha = 1,
  col.bg = NULL,
  col.bg.alpha = 1,
  col.inner.label.circle = NULL,
  inner.label.circle.width = "default",
  col.outer.label.circle = NULL,
  outer.label.circle.width = "default",
  clockwise = FALSE,
  init.angle = if (clockwise) 90 else 0,
  angle = 360,
  pfmNameSpliter = ";",
  rcpostfix = "(RC)",
  motifScale = c("linear", "logarithmic"),
  ic.scale = TRUE,
  plotIndex = FALSE,
  IndexCol = "black",
  IndexCex = 0.8,
  groupDistance = NA,
  groupDistanceLineCol = "red",
  plotAxis = FALSE,
  font = "sans",
  ...
)

Arguments

`phylog`	an object of class phylog
`pfms`	a list of objects of class pfm
`circle`	a size coefficient for the outer circle of the labels. Please note this is the position of inner.label.cirle.
`circle.motif`	a size coefficient for the motif circle
`cleaves`	a character size for plotting the points that represent the leaves, used with par("cex")*cleaves. If zero, no points are drawn
`cnodes`	a character size for plotting the points that represent the nodes, used with par("cex")*cnodes. If zero, no points are drawn
`labels.leaves`	a vector of strings of characters for the leaves labels
`clabel.leaves`	a character size for the leaves labels, used with par("cex")*clabel.leaves
`labels.nodes`	a vector of strings of characters for the nodes labels
`clabel.nodes`	a character size for the nodes labels, used with par("cex")*clabel.nodes. If zero, no nodes labels are drawn
`draw.box`	if TRUE draws a box around the current plot with the function box()
`col.leaves`	a vector of colors for leaves labels
`col.leaves.bg`	a vector of colors for background of leaves labels
`col.leaves.bg.alpha`	alpha value [0, 1] for the colors of backgroud of leaves labels
`col.bg`	a vector of colors for tree background
`col.bg.alpha`	a alpha value [0, 1] of colors for tree background
`col.inner.label.circle`	a vector of colors for inner cirlce of pfms
`inner.label.circle.width`	width for inner circle of pfms
`col.outer.label.circle`	a vector of colors for outer circle of pfms
`outer.label.circle.width`	width for outer circle of pfms
`clockwise`	a logical value indicating if slices are drawn clockwise or counter clockwise
`init.angle`	number specifying the starting angle (in degrees) for the slices. Defaults to 0 (i.e., ‘3 o’clock') unless clockwise is true where init.angle defaults to 90 (degrees), (i.e., ‘12 o’clock')
`angle`	number specifying the angle (in degrees) for phylogenic tree. Defaults 360
`pfmNameSpliter`	spliter when name of pfms contain multiple node of labels.leaves
`rcpostfix`	the postfix for reverse complements
`motifScale`	the scale of logo size
`ic.scale`	logical. If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
`plotIndex`	logical. If TRUE, will plot index number in the motifLogo which can help user to describe the motifLogo
`IndexCol`	The color of the index number when plotIndex is TRUE.
`IndexCex`	The cex of the index number when plotIndex is TRUE.
`groupDistance`	show groupDistance on the draw
`groupDistanceLineCol`	groupDistance line color, default: red
`plotAxis`	logical. If TRUE, will plot distance axis.
`font`	font of logo
`...`	not used.

Value

none

Examples


  if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                            names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
    library(RColorBrewer)
    color <- brewer.pal(12, "Set3")
    plotMotifStackWithRadialPhylog(phylog, pfms, circle=0.9, 
                 cleaves = 0.5, clabel.leaves = 0.7, 
                 col.bg=rep(color, each=5), col.leaves=rep(color, each=5))
  }

if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", 
                            names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
    library(RColorBrewer)
    color <- brewer.pal(12, "Set3")
    plotMotifStackWithRadialPhylog(phylog, pfms, circle=0.9, 
                 cleaves = 0.5, clabel.leaves = 0.7, 
                 col.bg=rep(color, each=5), col.leaves=rep(color, each=5))
  }

plot x-axis

Description

plot x-axis for the sequence logo

Usage

plotXaxis(pfm, p = rep(0.25, 4), label = NULL)
plotXaxis(pfm, p = rep(0.25, 4), label = NULL)

Arguments

`pfm`	position frequency matrices
`p`	background possibility
`label`	x-axis labels

Value

none

plot y-axis

Description

plot y-axis for the sequence logo

Usage

plotYaxis(ymax, ic.scale)
plotYaxis(ymax, ic.scale)

Arguments

`ymax`	max value of y axix
`ic.scale`	Use IC scale or not. See plotMotifLogo for help.

Value

none

Class `"psam"`

Description

An object of class "psam" represents the position specific affinity matrix (PSAM) of a DNA/RNA/amino-acid sequence motif. The entry stores a matrix, which in row i, column j gives the affinity of observing nucleotide/or amino acid i in position j of the motif.

methods for psam objects.

Usage

## S4 method for signature 'psam'
x$name

## S4 method for signature 'psam,ANY'
plot(x, y = "missing", ...)

## S4 method for signature 'psam'
matrixReverseComplement(x)

## S4 method for signature 'psam,numeric,logical'
addBlank(x, n, b)

## S4 method for signature 'psam'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'psam'
format(x, ...)
## S4 method for signature 'psam'
x$name

## S4 method for signature 'psam,ANY'
plot(x, y = "missing", ...)

## S4 method for signature 'psam'
matrixReverseComplement(x)

## S4 method for signature 'psam,numeric,logical'
addBlank(x, n, b)

## S4 method for signature 'psam'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'psam'
format(x, ...)

Arguments

`x`	An object of class `psam`.
`name`	Slot name.
`y`	Not use.
`...`	Further potential arguments passed to `plotAffinityLogo`.
`n`	how many spaces should be added.
`b`	logical value to indicate where the space should be added.
`row.names`, `optional`	see as.data.frame

Objects from the Class

Objects can be created by calls of the form new("psam", mat, name, alphabet, color).

Methods

addBlank: signature(x="psam", n="numeric", b="logical") add space into the position specific affinity matrix for alignment. b is a bool value, if TRUE, add space to the 3' end, else add space to the 5' end. n indicates how many spaces should be added.
matrixReverseComplement: signature(x = "psam") get the reverse complement of position specific affinity matrix.
plot: signature(x = "psam") Plots the affinity logo of the position specific affinity matrix.
$, $<-: Get or set the slot of psam-class
as.data.frame: convert psam-class to a data.frame
format: return the name_pfm of psam-class

Examples


motif <- importMatrix(file.path(find.package("motifStack"), "extdata", "PSAM.mxr"), 
         format="psam")[[1]]
plot(motif)


motif <- importMatrix(file.path(find.package("motifStack"), "extdata", "PSAM.mxr"), 
                      format="psam")[[1]]
matrixReverseComplement(motif)
addBlank(motif, 1, FALSE)
addBlank(motif, 3, TRUE)
as(motif,"matrix")
as.data.frame(motif)
format(motif)

motif <- importMatrix(file.path(find.package("motifStack"), "extdata", "PSAM.mxr"), 
         format="psam")[[1]]
plot(motif)


motif <- importMatrix(file.path(find.package("motifStack"), "extdata", "PSAM.mxr"), 
                      format="psam")[[1]]
matrixReverseComplement(motif)
addBlank(motif, 1, FALSE)
addBlank(motif, 3, TRUE)
as(motif,"matrix")
as.data.frame(motif)
format(motif)

Class `"pssm"`

Description

An object of class "pssm" represents the position specific score matrix of a DNA/RNA/amino-acid sequence motif. The entry stores a matrix, which in row i, column j gives the log-odds probability of nucleotide/or amino acid i in position j of the motif.

methods for pssm objects.

Usage

## S4 method for signature 'pssm'
x$name

## S4 method for signature 'pssm,ANY'
plot(x, y = "missing", ...)

## S4 method for signature 'pssm'
matrixReverseComplement(x)

## S4 method for signature 'pssm,numeric,logical'
addBlank(x, n, b)

## S4 method for signature 'pssm'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'pssm'
format(x, ...)
## S4 method for signature 'pssm'
x$name

## S4 method for signature 'pssm,ANY'
plot(x, y = "missing", ...)

## S4 method for signature 'pssm'
matrixReverseComplement(x)

## S4 method for signature 'pssm,numeric,logical'
addBlank(x, n, b)

## S4 method for signature 'pssm'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'pssm'
format(x, ...)

Arguments

`x`	An object of class `pssm`. For `getIC`, if parameter p is followed, x should be an object of matrix.
`name`	Slot name.
`y`	Not use.
`...`	Further potential arguments passed to `plotMotifLogo`.
`n`	how many spaces should be added.
`b`	logical value to indicate where the space should be added.
`row.names`, `optional`	see as.data.frame

Objects from the Class

Objects can be created by calls of the form new("pssm", mat, name, alphabet, color, background).

Methods

addBlank: signature(x="pssm", n="numeric", b="logical") add space into the position frequency matrix for alignment. b is a bool value, if TRUE, add space to the 3' end, else add space to the 5' end. n indicates how many spaces should be added.
matrixReverseComplement: signature(x = "pssm") get the reverse complement of position frequency matrix.
plot: signature(x = "pssm") Plots the sequence logo of the position frequency matrix.
$, $<-: Get or set the slot of pssm-class
as.data.frame: convert pssm-class to a data.frame
format: return the name_pssm of pssm-class

Examples


pcm <- read.table(file.path(find.package("motifStack"), 
                            "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- pcm2pssm(pcm)
motif <- new("pssm", mat=motif, name="bin_SOLEXA")
plot(motif)


pcm <- read.table(file.path(find.package("motifStack"), 
                  "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- pcm2pssm(pcm)
motif <- new("pssm", mat=motif, name="bin_SOLEXA")
matrixReverseComplement(motif)
addBlank(motif, 1, FALSE)
addBlank(motif, 3, TRUE)
as(motif,"matrix")
as.data.frame(motif)
format(motif)

pcm <- read.table(file.path(find.package("motifStack"), 
                            "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- pcm2pssm(pcm)
motif <- new("pssm", mat=motif, name="bin_SOLEXA")
plot(motif)


pcm <- read.table(file.path(find.package("motifStack"), 
                  "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- pcm2pssm(pcm)
motif <- new("pssm", mat=motif, name="bin_SOLEXA")
matrixReverseComplement(motif)
addBlank(motif, 1, FALSE)
addBlank(motif, 3, TRUE)
as(motif,"matrix")
as.data.frame(motif)
format(motif)

read pcm from a path

Description

read position count matrix from a path

Usage

readPCM(path = ".", pattern = NULL)
readPCM(path = ".", pattern = NULL)

Arguments

`path`	a character vector of full path names
`pattern`	an optional regular expression

Value

A list of pcm objects

Examples


pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")

pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")

re-order UPGMA tree

Description

re-order the UPGMA tree by adjacent motif distance

Usage

reorderUPGMAtree(phylog, motifs, rcpostfix = "(RC)")
reorderUPGMAtree(phylog, motifs, rcpostfix = "(RC)")

Arguments

`phylog`	an object of phylog
`motifs`	a list of objects of pfm
`rcpostfix`	the postfix for reverse complements

Value

an object of phylog

Author(s)

Jianhong Ou

Examples


  if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    reorderUPGMAtree(phylog, pfms)
  }

if(interactive() || Sys.getenv("USER")=="jianhongou"){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    reorderUPGMAtree(phylog, pfms)
  }

traceback global

Description

traceback global

Usage

traceBackGlobal(dpScore, score, m, n)
traceBackGlobal(dpScore, score, m, n)

Arguments

`dpScore`	Dynamic programming score
`score`	ALLR scores
`m`, `n`	matrix width

Value

a data.frame

traceback local

Description

traceback local

Usage

traceBackLocal(dpScore, score, m, n)
traceBackLocal(dpScore, score, m, n)

Arguments

`dpScore`	Dynamic programming score matrix
`score`	ALLR scores, m x n matrix
`m`, `n`	matrix width

Value

a data.frame

Package 'motifStack'

Help Index

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

Description

Author(s)

align AA motifs

Description

Usage

Arguments

Value

Examples

browse motifs

Description

Usage

Arguments

Value

Examples

Shiny bindings for browseMotifs

Description

Usage

Arguments

calculate frequence

Description

Usage

Arguments

Value

calculate I'

Description

Usage

Arguments

Value

cluster motifs

Description

Usage

Arguments

Value

Examples

retrieve color setting for logo

Description

Usage

Arguments

Value

Examples

compare two profiles

Description

Usage

Arguments

Value

comapre w pcm

Description

Usage

Arguments

Value

align DNA motifs

Description

Usage

Arguments

Value

Examples

convert DNA motif into RNA motif

Description

Usage

Arguments

Value

Examples

Global alignment version

Description

Usage

Arguments

Value

Dynamic programming function, local version

Description

Usage

Arguments

Value

geom_motif

Description

Usage

Arguments

Value

Class `marker`