R/plotMotifLogo.R
In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Defines functions
geom_motif
motifGrob
plotMarkers
plotMotifLogoA
plotYaxis
plotXaxis
plotMotifLogo
Documented in
geom_motif
motifGrob
plotMotifLogo
plotMotifLogoA
plotXaxis
plotYaxis
#' plot sequence logo
#'
#' plot amino acid or DNA sequence logo
#'
#'
#' @param pfm a position frequency matrices
#' @param motifName motif name
#' @param p background possibility
#' @param font font of logo
#' @param fontface fontface of logo
#' @param colset color setting for each logo letter
#' @param 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.
#' @param yaxis draw y-axis or not
#' @param xlab x-label, do nothing if set xlab as NA
#' @param ylab y-label, do nothing if set ylab as NA
#' @param xlcex cex value for x-label
#' @param ylcex cex value for y-label
#' @param ncex cex value for motif name
#' @param 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.
#' @param newpage logical If TRUE, plot it in a new page.
#' @param margins A numeric vector interpreted in the same way as par(mar) in
#' base graphics.
#' @param draw Vector (logical(1)). TRUE to plot. FALSE, return a gList
#' @param ... Not used.
#' @return none
#' @export
#' @importFrom grid gList gTree plotViewport textGrob unit gpar grid.newpage
#' grid.draw gList grid.draw pointsGrob
#' @examples
#'
#' pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
#' pfm<-pcm2pfm(pcm)
#' rownames(pfm)<-c("A","C","G","T")
#' plotMotifLogo(pfm)
#'
plotMotifLogo<-function(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, .1), draw=TRUE,
...){
markers <- NULL
if (is(pfm, "data.frame")){
pfm <- as.matrix(pfm)
}else{
if(is(pfm, "pcm")){
pfm <- pcm2pfm(pfm)
}
if(is(pfm, "pfm")){
markers <- pfm@markers
if(missing(motifName)) motifName = pfm@name
p=pfm@background[rownames(pfm@mat)]
p <- p/sum(p)
colset=pfm@color[rownames(pfm@mat)]
pfm <- pfm@mat
}
}
if (!is(pfm, "matrix")){
stop("pfm must be a matrix")
}
if(length(p)<nrow(pfm)){
warning("background length is shorter than number of rows. Will use default background")
p <- rep(1/nrow(pfm), nrow(pfm))
}
if (any(abs(1 - apply(pfm,2,sum)) > 0.01))
stop("Columns of pfm must add up to 1.0")
if(!is(colset, "character"))
stop("colset must be character")
if (length(colset)!=nrow(pfm))
stop(paste("colset length and pfm row numbers different",length(colset),"!=",nrow(pfm)))
rname<-rownames(pfm)
if(is.null(rname))
stop("pfm rowname is empty")
npos<-ncol(pfm)
ncha<-nrow(pfm)
key<-paste("x", ncha, font, paste(colset, collapse=""), paste(rname, collapse=""), sep="_")
symbolsCache <- if(exists("tmp_motifStack_symbolsCache", envir=.globals)) get("tmp_motifStack_symbolsCache", envir=.globals) else list()
if(!is.null(symbolsCache[[key]])) symbols<-symbolsCache[[key]]
else {
symbols<-coloredSymbols(ncha, font, colset, rname, fontface=fontface)
symbolsCache[[key]]<-symbols
assign("tmp_motifStack_symbolsCache", symbolsCache, envir=.globals)
}
pictureGrob <- get("pictureGrob", envir = .globals)
#calculate postion of each symbol and plot
plot <- gList()
ic<-getIC(pfm, p)
if(ic.scale[1]){
ie<-getIE(pfm)
ie <- max(c(ie, ic))
}else{
ie <- 1
}
dw<-1/npos
x.pos<-0
y.poss <- numeric(length=npos)
for(j in 1:npos){
column<-pfm[,j]
if(ic.scale[1]){
heights<-column*ic[j]/ie
}else{
heights <- column
}
id<-order(heights)
y.pos<-0
for(i in 1:ncha){
h<-heights[id[i]]
if(h>0 && ic[j]>0) plot <-
gList(plot,
pictureGrob(picture=symbols[[id[i]]],
x=x.pos,
y=y.pos,
width = dw,
height = h,
just=c(0,0),
distort=TRUE))
y.pos<-y.pos+h
}
y.poss[j] <- y.pos
x.pos<-x.pos+dw
}
if(length(markers)>0){
plot <- gList(plot, plotMarkers(markers, dw, y.poss))
}
if(is.logical(xaxis)){
if(xaxis[1]){
plot <- gList(plot, plotXaxis(pfm, p))
}
}else{
if(length(xaxis)){
plot <- gList(plot, plotXaxis(pfm, p, label=xaxis))
}
}
if(yaxis) plot <- gList(plot, plotYaxis(ie, ic.scale))
plot <- gTree(children=plot,
vp= plotViewport(margins = margins))
if(!is.na(xlab)) plot <- gList(plot, textGrob(xlab, y=unit(1, units = "lines"), gp=gpar(cex=xlcex), name="xlab"))
if(!is.na(ylab)) plot <- gList(plot, textGrob(ylab, x=unit(1, units = "lines"), gp=gpar(cex=ylcex), rot=90, name="ylab"))
if(!missing(motifName)) plot <- gList(plot, textGrob(motifName,y=unit(1, "npc")-unit(.5, units = "lines"), gp=gpar(cex=ncex), name="motifName"))
if(draw){
if(newpage) grid.newpage()
suppressWarnings(grid.draw(plot))
}else{
plot
}
}
#' plot x-axis
#'
#' plot x-axis for the sequence logo
#'
#'
#' @param pfm position frequency matrices
#' @param p background possibility
#' @param label x-axis labels
#' @return none
#' @importFrom grid xaxisGrob gpar unit
plotXaxis<-function(pfm, p=rep(0.25, 4), label=NULL){
npos<-ncol(pfm)
ic<-getIC(pfm,p)
dw<-1/npos
at<-c()
label_j <- c()
j=1
for(i in seq.int(npos)){
if(ic[i]>0){
at<-c(at,dw*(i-0.5))
label_j<-c(label_j,j)
j<-j+1
}
}
if(length(label)!=length(at)){
label <- label_j
}
grob <- xaxisGrob(at=at,label=label, gp=gpar(lwd=1, lex=1, lineheight=1))
grob$children$labels$y <- unit(-1.1, "lines")
grob
}
#' plot y-axis
#'
#' plot y-axis for the sequence logo
#'
#'
#' @param ymax max value of y axix
#' @param ic.scale Use IC scale or not. See plotMotifLogo for help.
#' @return none
#' @importFrom grid yaxisGrob gpar unit gList convertUnit
plotYaxis<-function(ymax, ic.scale){
ie <- ymax
interval <- 5
majorat<-seq(0,floor(ie),length.out = interval)
majorat <- majorat/ie
majorlab<-seq(0,floor(ie),length.out = interval)
if(!ic.scale[1]){
if(length(ic.scale)>1){
if(is.numeric(ic.scale[1])){
majorlab <- majorlab*ic.scale[2]
}
}
}
majorY <- yaxisGrob(at=majorat,label=majorlab,
name = "majorY",
gp=gpar(lwd=1, lex=1, lineheight=1))
YgList <- gList(majorY)
if(convertUnit(unit(1, "npc"), unitTo = "lines", valueOnly = TRUE) > 10){
minorat<-seq(0, floor(ie), length.out = (interval-1)*5+1)
minorat <- seq(0, ie, by=diff(minorat)[1])
minorat <- minorat/ie
minorat<-minorat[!(minorat %in% majorat)]
minorY <- yaxisGrob(at=minorat,label=FALSE,name="minorY",
gp=gpar(lwd=1, lineheight=.5))
at <- c(min(c(minorat, majorat)), max(c(minorat, majorat)))
terminY <- yaxisGrob(at=at, label=FALSE, name="endY",
gp=gpar(lwd=1, lineheight=.5))
YgList <- gList(YgList, minorY, terminY)
}
YgList
}
###############################################################################
######## plot motif logo without plot.new
######## to be used to create a better view of stack, eg. radial sty,
###############################################################################
#' plot sequence logo without plot.new
#'
#' plot amino acid or DNA sequence logo in a given canvas
#'
#'
#' @param pfm an object of pfm
#' @param font font of logo
#' @param fontface fontface of logo
#' @param ic.scale logical If TRUE, the height of each column is proportional
#' to its information content. Otherwise, all columns have the same height.
#' @param draw Vector (logical(1)). TRUE to plot. FALSE, return a gList
#' @return none
#' @export
#' @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)
#'
plotMotifLogoA<-function(pfm, font="sans", fontface="bold", ic.scale=TRUE, draw=TRUE){
if (is(pfm, "pcm")){
pfm <- pcm2pfm(pfm)
}
if (!is(pfm, "pfm")){
stop("pfms must be a pfm object")
}
rname<-rownames(pfm@mat)
if(is.null(rname))
stop("pfm rowname is empty")
npos<-ncol(pfm@mat)
ncha<-nrow(pfm@mat)
key<-paste("x", ncha, font, paste(pfm@color, collapse=""), paste(rname, collapse=""), sep="_")
symbolsCache <- if(exists("tmp_motifStack_symbolsCache", envir=.globals)) get("tmp_motifStack_symbolsCache", envir=.globals) else list()
if(!is.null(symbolsCache[[key]])) symbols<-symbolsCache[[key]]
else {
symbols<-coloredSymbols(ncha, font, pfm@color, rname, fontface=fontface)
symbolsCache[[key]]<-symbols
assign("tmp_motifStack_symbolsCache", symbolsCache, envir=.globals)
}
pictureGrob <- get("pictureGrob", envir = .globals)
#calculate postion of each symbol and plot
plot <- gList()
ic<-getIC(pfm)
ie<-getIE(pfm@mat)
ie <- max(c(ie, ic))
dw<-1/npos
x.pos<-0
y.poss <- numeric(length=npos)
for(j in 1:npos){
column<-pfm@mat[,j]
if(ic.scale){
heights<-column*ic[j]/ie
}else{
heights <- column
}
id<-order(heights)
y.pos<-0
for(i in 1:ncha){
h<-heights[id[i]]
if(h>0 && ic[j]>0) plot <-
gList(plot,
pictureGrob(picture = symbols[[id[i]]],
x = x.pos,
y = y.pos,
width = dw,
height = h,
just=c(0,0),
distort=TRUE))
y.pos<-y.pos+h
}
y.poss[j] <- y.pos
x.pos<-x.pos+dw
}
markers <- pfm@markers
if(length(markers)>0){
plot <- gList(plot, plotMarkers(markers, dw, y.poss))
}
if(draw){
suppressWarnings(grid.draw(plot))
}else{
plot
}
}
#' @importFrom grid gList rectGrob textGrob linesGrob segmentsGrob
plotMarkers <- function(markers, dw, h, lo=NULL){
do.call(gList, lapply(markers, function(m){
switch(m@type,
"rect"={
pos <- mapply(seq, m@start, m@stop, SIMPLIFY = FALSE)
if(length(lo)>0 && length(lo)==length(h)){
height <- sapply(pos, function(.ele) max(h[.ele])-min(lo[.ele]))
y <- sapply(pos, function(.ele) (min(lo[.ele])+max(h[.ele]))/2)
}else{
height <- sapply(pos, function(.ele) max(h[.ele]))
y <- height/2
}
res <- rectGrob(x= (m@start + m@stop-1)*dw/2,
y = y,
width = dw*(m@stop - m@start + 1),
height = height,
gp = m@gp)
if(any(nchar(m@label)>0)){
tG <- textGrob(label=m@label,
x = (m@start+m@stop-1)*dw/2,
y = height,
vjust = -.5,
gp = m@gp)
res <- gList(res, tG)
}
res
},
"text"={
pos <- mapply(seq, m@start, m@stop, SIMPLIFY = FALSE)
label <- rep(m@label, lengths(pos))
pos <- unlist(pos)
textGrob(label=label,
x = (pos-.5)*dw,
y = h[pos],
vjust = -0.1,
gp = m@gp)
},
"line"={
pos <- mapply(seq, m@start, m@stop, SIMPLIFY = FALSE)
height <- sapply(pos, function(.ele) max(h[.ele]))
res <- segmentsGrob(x0 = (m@start-1)*dw,
x1 = m@stop*dw,
y0 = height,
y1 = height,
gp = m@gp)
if(any(nchar(m@label)>0)){
tG <- textGrob(label=m@label,
x = (m@start+m@stop-1)*dw/2,
y = height,
vjust = -.5,
gp = m@gp)
res <- gList(res, tG)
}
res
})
}))
}
################## for ggplot2 ###################
#' Motif Grob
#'
#' This function create a motif grob.
#'
#'
#' @param pfm an object of pfm
#' @param x A numeric vector or unit object specifying x-values.
#' @param y A numeric vector or unit object specifying y-values.
#' @param width A numeric vector or unit object specifying width.
#' @param height A numeric vector or unit object specifying height.
#' @param 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.
#' @param ic.scale logical If TRUE, the height of each column is proportional
#' to its information content. Otherwise, all columns have the same height.
#' @param default.units A string indicating the default units to use if x, y,
#' width, or height are only given as numeric vectors.
#' @param name A character value to uniquely identify the motifGrob once it has
#' been pushed onto the grob tree.
#' @param gp A gpar object, typically the output from a call to the function
#' gpar. The list will be used as parameter of plotMotifLogoA.
#' @return An gTree object.
#' @author Jianhong Ou
#' @export
#' @importFrom grid unit gpar viewport gTree
#' @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)
#'
motifGrob <- function(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")){
vp <- viewport(x=x, y=y, width = width, height = height,
default.units = default.units, angle = angle, name = "motifVP")
fontfamily <- ifelse(length(gp$fontfamily)>0, gp$fontfamily[1], "sans")
fontface <- ifelse(length(gp$fontface)>0, gp$fontface[1], "bold")
gTree(children=plotMotifLogoA(pfm, font = fontfamily, fontface = fontface, ic.scale = ic.scale, draw=FALSE),
name=name, vp=vp, cl="motif")
}
#' geom_motif
#'
#' geom_motif uses the locations of the four corners (xmin, xmax, ymin and
#' ymax) to plot motifs.
#'
#'
#' @param 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.
#' @param data The data to be displayed in this layer.
#' @param stat The statistical transformation to use on the data for this
#' layer, as a string.
#' @param position Position adjustment, either as a string, or the result of a
#' call to a position adjustment function.
#' @param \dots Other arguments passed on to layer().
#' @param ic.scale logical If TRUE, the height of each column is proportional
#' to its information content. Otherwise, all columns have the same height.
#' @param use.xy logical If TRUE, the required aesthethics will be x, y, width,
#' height, and motif. Otherwise, xmin, ymin, xmax, ymax and motif.
#' @param show.legend Not used.
#' @param inherit.aes If FALSE, overrides the default aesthetics, rather than
#' combining with them.
#' @return a layer that contains GeomMotif object.
#' @section Aesthetics: geom_motif() understands the following aesthetics
#' (required aesthetics are in bold): \itemize{ \item \strong{\code{xmin}}
#' \item \strong{\code{xmax}} \item \strong{\code{ymin}} \item
#' \strong{\code{ymax}} \item \strong{\code{motif}} \item \code{angle} \item
#' \code{fontfamily} \item \code{fontface} }
#'
#' OR
#'
#' \itemize{ \item \strong{\code{x}} \item \strong{\code{y}} \item
#' \strong{\code{width}} \item \strong{\code{height}} \item
#' \strong{\code{motif}} \item \code{angle} \item \code{fontfamily} \item
#' \code{fontface} }
#' @author Jianhong Ou
#' @export
#' @importFrom ggplot2 layer
#' @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)
#'
geom_motif <- function(mapping = NULL, data = NULL,
stat = "identity", position = "identity",
...,
ic.scale=TRUE,
use.xy=FALSE,
show.legend = NA,
inherit.aes = TRUE) {
layer(
data = data,
mapping = mapping,
stat = stat,
geom = if(use.xy) GeomMotifA else GeomMotif,
position = position,
show.legend = show.legend,
inherit.aes = inherit.aes,
params = list(
ic.scale = ic.scale,
...
)
)
}
#' GeomMotif object
#'
#' GeomMotif object is a ggproto object.
#'
#'
#' @name 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>
#' @seealso geom_motif
#' @export
#' @importFrom ggplot2 ggproto aes Geom
#' @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$motif <- list(pcm2pfm(motif), pcm2pfm(motif))
#'
#' library(ggplot2)
#'
#' ggplot(df, aes(xmin=xmin, ymin=ymin, xmax=xmax, ymax=ymax, motif=motif)) +
#' geom_motif() + theme_bw() + ylim(0, 1) + xlim(0, 1)
#'
#'
GeomMotif <-
ggproto("GeomMotif", Geom,
required_aes = c("xmin", "ymin", "xmax", "ymax", "motif"),
default_aes = aes(angle=0, fontfamily="sans",
fontface="bold"),
draw_panel = function(data, panel_params, coord, ic.scale=TRUE){
coords <- coord$transform(data, panel_params)
n <- nrow(coords)
do.call(gList, lapply(seq.int(n), function(.id){
motifGrob(pfm=coords$motif[[.id]],
x=mean(c(coords$xmin[.id], coords$xmax[.id])),
y=mean(c(coords$ymin[.id], coords$ymax[.id])),
width=coords$xmax[.id] - coords$xmin[.id],
height=coords$ymax[.id] - coords$ymin[.id],
angle=coords$angle[.id], ic.scale=ic.scale,
default.units = "native",
gp = gpar(fontfamily=coords$fontfamily[.id],
fontface=coords$fontface[.id]),
name = paste0("geom_motif_", .id))
}))
})
GeomMotifA <-
ggproto("GeomMotif", Geom,
required_aes = c("x", "y", "width", "height", "motif"),
default_aes = aes(angle=0, fontfamily="sans",
fontface="bold"),
draw_panel = function(data, panel_params, coord, ic.scale=TRUE){
if(is.unit(data$x)) data$x <- convertUnit(data$x, unitTo = "native", valueOnly = TRUE)
if(is.unit(data$y)) data$y <- convertUnit(data$x, unitTo = "native", valueOnly = TRUE)
if(is.unit(data$width)) data$width <- convertUnit(data$width, unitTo = "native", valueOnly = TRUE)
if(is.unit(data$height)) data$height <- convertUnit(data$height, unitTo = "native", valueOnly = TRUE)
hw <- data$width/2
hh <- data$height/2
data$xmin <- data$x - hw
data$ymin <- data$y - hh
data$xmax <- data$x + hw
data$ymax <- data$y + hh
coords <- coord$transform(data, panel_params)
n <- nrow(coords)
do.call(gList, lapply(seq.int(n), function(.id){
motifGrob(pfm=coords$motif[[.id]],
x=mean(c(coords$xmin[.id], coords$xmax[.id])),
y=mean(c(coords$ymin[.id], coords$ymax[.id])),
width=coords$xmax[.id] - coords$xmin[.id],
height=coords$ymax[.id] - coords$ymin[.id],
angle=coords$angle[.id], ic.scale=ic.scale,
default.units = "native",
gp = gpar(fontfamily=coords$fontfamily[.id],
fontface=coords$fontface[.id]),
name = paste0("geom_motif_", .id))
}))
})
jianhong/motifStack documentation built on Nov. 5, 2024, 7:47 a.m.
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Defines functions geom_motif motifGrob plotMarkers plotMotifLogoA plotYaxis plotXaxis plotMotifLogo
Documented in geom_motif motifGrob plotMotifLogo plotMotifLogoA plotXaxis plotYaxis
#' plot sequence logo
#'
#' plot amino acid or DNA sequence logo
#'
#'
#' @param pfm a position frequency matrices
#' @param motifName motif name
#' @param p background possibility
#' @param font font of logo
#' @param fontface fontface of logo
#' @param colset color setting for each logo letter
#' @param 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.
#' @param yaxis draw y-axis or not
#' @param xlab x-label, do nothing if set xlab as NA
#' @param ylab y-label, do nothing if set ylab as NA
#' @param xlcex cex value for x-label
#' @param ylcex cex value for y-label
#' @param ncex cex value for motif name
#' @param 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.
#' @param newpage logical If TRUE, plot it in a new page.
#' @param margins A numeric vector interpreted in the same way as par(mar) in
#' base graphics.
#' @param draw Vector (logical(1)). TRUE to plot. FALSE, return a gList
#' @param ... Not used.
#' @return none
#' @export
#' @importFrom grid gList gTree plotViewport textGrob unit gpar grid.newpage
#' grid.draw gList grid.draw pointsGrob
#' @examples
#'
#' pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
#' pfm<-pcm2pfm(pcm)
#' rownames(pfm)<-c("A","C","G","T")
#' plotMotifLogo(pfm)
#'
plotMotifLogo<-function(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, .1), draw=TRUE,
...){
markers <- NULL
if (is(pfm, "data.frame")){
pfm <- as.matrix(pfm)
}else{
if(is(pfm, "pcm")){
pfm <- pcm2pfm(pfm)
}
if(is(pfm, "pfm")){
markers <- pfm@markers
if(missing(motifName)) motifName = pfm@name
p=pfm@background[rownames(pfm@mat)]
p <- p/sum(p)
colset=pfm@color[rownames(pfm@mat)]
pfm <- pfm@mat
}
}
if (!is(pfm, "matrix")){
stop("pfm must be a matrix")
}
if(length(p)<nrow(pfm)){
warning("background length is shorter than number of rows. Will use default background")
p <- rep(1/nrow(pfm), nrow(pfm))
}
if (any(abs(1 - apply(pfm,2,sum)) > 0.01))
stop("Columns of pfm must add up to 1.0")
if(!is(colset, "character"))
stop("colset must be character")
if (length(colset)!=nrow(pfm))
stop(paste("colset length and pfm row numbers different",length(colset),"!=",nrow(pfm)))
rname<-rownames(pfm)
if(is.null(rname))
stop("pfm rowname is empty")
npos<-ncol(pfm)
ncha<-nrow(pfm)
key<-paste("x", ncha, font, paste(colset, collapse=""), paste(rname, collapse=""), sep="_")
symbolsCache <- if(exists("tmp_motifStack_symbolsCache", envir=.globals)) get("tmp_motifStack_symbolsCache", envir=.globals) else list()
if(!is.null(symbolsCache[[key]])) symbols<-symbolsCache[[key]]
else {
symbols<-coloredSymbols(ncha, font, colset, rname, fontface=fontface)
symbolsCache[[key]]<-symbols
assign("tmp_motifStack_symbolsCache", symbolsCache, envir=.globals)
}
pictureGrob <- get("pictureGrob", envir = .globals)
#calculate postion of each symbol and plot
plot <- gList()
ic<-getIC(pfm, p)
if(ic.scale[1]){
ie<-getIE(pfm)
ie <- max(c(ie, ic))
}else{
ie <- 1
}
dw<-1/npos
x.pos<-0
y.poss <- numeric(length=npos)
for(j in 1:npos){
column<-pfm[,j]
if(ic.scale[1]){
heights<-column*ic[j]/ie
}else{
heights <- column
}
id<-order(heights)
y.pos<-0
for(i in 1:ncha){
h<-heights[id[i]]
if(h>0 && ic[j]>0) plot <-
gList(plot,
pictureGrob(picture=symbols[[id[i]]],
x=x.pos,
y=y.pos,
width = dw,
height = h,
just=c(0,0),
distort=TRUE))
y.pos<-y.pos+h
}
y.poss[j] <- y.pos
x.pos<-x.pos+dw
}
if(length(markers)>0){
plot <- gList(plot, plotMarkers(markers, dw, y.poss))
}
if(is.logical(xaxis)){
if(xaxis[1]){
plot <- gList(plot, plotXaxis(pfm, p))
}
}else{
if(length(xaxis)){
plot <- gList(plot, plotXaxis(pfm, p, label=xaxis))
}
}
if(yaxis) plot <- gList(plot, plotYaxis(ie, ic.scale))
plot <- gTree(children=plot,
vp= plotViewport(margins = margins))
if(!is.na(xlab)) plot <- gList(plot, textGrob(xlab, y=unit(1, units = "lines"), gp=gpar(cex=xlcex), name="xlab"))
if(!is.na(ylab)) plot <- gList(plot, textGrob(ylab, x=unit(1, units = "lines"), gp=gpar(cex=ylcex), rot=90, name="ylab"))
if(!missing(motifName)) plot <- gList(plot, textGrob(motifName,y=unit(1, "npc")-unit(.5, units = "lines"), gp=gpar(cex=ncex), name="motifName"))
if(draw){
if(newpage) grid.newpage()
suppressWarnings(grid.draw(plot))
}else{
plot
}
}
#' plot x-axis
#'
#' plot x-axis for the sequence logo
#'
#'
#' @param pfm position frequency matrices
#' @param p background possibility
#' @param label x-axis labels
#' @return none
#' @importFrom grid xaxisGrob gpar unit
plotXaxis<-function(pfm, p=rep(0.25, 4), label=NULL){
npos<-ncol(pfm)
ic<-getIC(pfm,p)
dw<-1/npos
at<-c()
label_j <- c()
j=1
for(i in seq.int(npos)){
if(ic[i]>0){
at<-c(at,dw*(i-0.5))
label_j<-c(label_j,j)
j<-j+1
}
}
if(length(label)!=length(at)){
label <- label_j
}
grob <- xaxisGrob(at=at,label=label, gp=gpar(lwd=1, lex=1, lineheight=1))
grob$children$labels$y <- unit(-1.1, "lines")
grob
}
#' plot y-axis
#'
#' plot y-axis for the sequence logo
#'
#'
#' @param ymax max value of y axix
#' @param ic.scale Use IC scale or not. See plotMotifLogo for help.
#' @return none
#' @importFrom grid yaxisGrob gpar unit gList convertUnit
plotYaxis<-function(ymax, ic.scale){
ie <- ymax
interval <- 5
majorat<-seq(0,floor(ie),length.out = interval)
majorat <- majorat/ie
majorlab<-seq(0,floor(ie),length.out = interval)
if(!ic.scale[1]){
if(length(ic.scale)>1){
if(is.numeric(ic.scale[1])){
majorlab <- majorlab*ic.scale[2]
}
}
}
majorY <- yaxisGrob(at=majorat,label=majorlab,
name = "majorY",
gp=gpar(lwd=1, lex=1, lineheight=1))
YgList <- gList(majorY)
if(convertUnit(unit(1, "npc"), unitTo = "lines", valueOnly = TRUE) > 10){
minorat<-seq(0, floor(ie), length.out = (interval-1)*5+1)
minorat <- seq(0, ie, by=diff(minorat)[1])
minorat <- minorat/ie
minorat<-minorat[!(minorat %in% majorat)]
minorY <- yaxisGrob(at=minorat,label=FALSE,name="minorY",
gp=gpar(lwd=1, lineheight=.5))
at <- c(min(c(minorat, majorat)), max(c(minorat, majorat)))
terminY <- yaxisGrob(at=at, label=FALSE, name="endY",
gp=gpar(lwd=1, lineheight=.5))
YgList <- gList(YgList, minorY, terminY)
}
YgList
}
###############################################################################
######## plot motif logo without plot.new
######## to be used to create a better view of stack, eg. radial sty,
###############################################################################
#' plot sequence logo without plot.new
#'
#' plot amino acid or DNA sequence logo in a given canvas
#'
#'
#' @param pfm an object of pfm
#' @param font font of logo
#' @param fontface fontface of logo
#' @param ic.scale logical If TRUE, the height of each column is proportional
#' to its information content. Otherwise, all columns have the same height.
#' @param draw Vector (logical(1)). TRUE to plot. FALSE, return a gList
#' @return none
#' @export
#' @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)
#'
plotMotifLogoA<-function(pfm, font="sans", fontface="bold", ic.scale=TRUE, draw=TRUE){
if (is(pfm, "pcm")){
pfm <- pcm2pfm(pfm)
}
if (!is(pfm, "pfm")){
stop("pfms must be a pfm object")
}
rname<-rownames(pfm@mat)
if(is.null(rname))
stop("pfm rowname is empty")
npos<-ncol(pfm@mat)
ncha<-nrow(pfm@mat)
key<-paste("x", ncha, font, paste(pfm@color, collapse=""), paste(rname, collapse=""), sep="_")
symbolsCache <- if(exists("tmp_motifStack_symbolsCache", envir=.globals)) get("tmp_motifStack_symbolsCache", envir=.globals) else list()
if(!is.null(symbolsCache[[key]])) symbols<-symbolsCache[[key]]
else {
symbols<-coloredSymbols(ncha, font, pfm@color, rname, fontface=fontface)
symbolsCache[[key]]<-symbols
assign("tmp_motifStack_symbolsCache", symbolsCache, envir=.globals)
}
pictureGrob <- get("pictureGrob", envir = .globals)
#calculate postion of each symbol and plot
plot <- gList()
ic<-getIC(pfm)
ie<-getIE(pfm@mat)
ie <- max(c(ie, ic))
dw<-1/npos
x.pos<-0
y.poss <- numeric(length=npos)
for(j in 1:npos){
column<-pfm@mat[,j]
if(ic.scale){
heights<-column*ic[j]/ie
}else{
heights <- column
}
id<-order(heights)
y.pos<-0
for(i in 1:ncha){
h<-heights[id[i]]
if(h>0 && ic[j]>0) plot <-
gList(plot,
pictureGrob(picture = symbols[[id[i]]],
x = x.pos,
y = y.pos,
width = dw,
height = h,
just=c(0,0),
distort=TRUE))
y.pos<-y.pos+h
}
y.poss[j] <- y.pos
x.pos<-x.pos+dw
}
markers <- pfm@markers
if(length(markers)>0){
plot <- gList(plot, plotMarkers(markers, dw, y.poss))
}
if(draw){
suppressWarnings(grid.draw(plot))
}else{
plot
}
}
#' @importFrom grid gList rectGrob textGrob linesGrob segmentsGrob
plotMarkers <- function(markers, dw, h, lo=NULL){
do.call(gList, lapply(markers, function(m){
switch(m@type,
"rect"={
pos <- mapply(seq, m@start, m@stop, SIMPLIFY = FALSE)
if(length(lo)>0 && length(lo)==length(h)){
height <- sapply(pos, function(.ele) max(h[.ele])-min(lo[.ele]))
y <- sapply(pos, function(.ele) (min(lo[.ele])+max(h[.ele]))/2)
}else{
height <- sapply(pos, function(.ele) max(h[.ele]))
y <- height/2
}
res <- rectGrob(x= (m@start + m@stop-1)*dw/2,
y = y,
width = dw*(m@stop - m@start + 1),
height = height,
gp = m@gp)
if(any(nchar(m@label)>0)){
tG <- textGrob(label=m@label,
x = (m@start+m@stop-1)*dw/2,
y = height,
vjust = -.5,
gp = m@gp)
res <- gList(res, tG)
}
res
},
"text"={
pos <- mapply(seq, m@start, m@stop, SIMPLIFY = FALSE)
label <- rep(m@label, lengths(pos))
pos <- unlist(pos)
textGrob(label=label,
x = (pos-.5)*dw,
y = h[pos],
vjust = -0.1,
gp = m@gp)
},
"line"={
pos <- mapply(seq, m@start, m@stop, SIMPLIFY = FALSE)
height <- sapply(pos, function(.ele) max(h[.ele]))
res <- segmentsGrob(x0 = (m@start-1)*dw,
x1 = m@stop*dw,
y0 = height,
y1 = height,
gp = m@gp)
if(any(nchar(m@label)>0)){
tG <- textGrob(label=m@label,
x = (m@start+m@stop-1)*dw/2,
y = height,
vjust = -.5,
gp = m@gp)
res <- gList(res, tG)
}
res
})
}))
}
################## for ggplot2 ###################
#' Motif Grob
#'
#' This function create a motif grob.
#'
#'
#' @param pfm an object of pfm
#' @param x A numeric vector or unit object specifying x-values.
#' @param y A numeric vector or unit object specifying y-values.
#' @param width A numeric vector or unit object specifying width.
#' @param height A numeric vector or unit object specifying height.
#' @param 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.
#' @param ic.scale logical If TRUE, the height of each column is proportional
#' to its information content. Otherwise, all columns have the same height.
#' @param default.units A string indicating the default units to use if x, y,
#' width, or height are only given as numeric vectors.
#' @param name A character value to uniquely identify the motifGrob once it has
#' been pushed onto the grob tree.
#' @param gp A gpar object, typically the output from a call to the function
#' gpar. The list will be used as parameter of plotMotifLogoA.
#' @return An gTree object.
#' @author Jianhong Ou
#' @export
#' @importFrom grid unit gpar viewport gTree
#' @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)
#'
motifGrob <- function(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")){
vp <- viewport(x=x, y=y, width = width, height = height,
default.units = default.units, angle = angle, name = "motifVP")
fontfamily <- ifelse(length(gp$fontfamily)>0, gp$fontfamily[1], "sans")
fontface <- ifelse(length(gp$fontface)>0, gp$fontface[1], "bold")
gTree(children=plotMotifLogoA(pfm, font = fontfamily, fontface = fontface, ic.scale = ic.scale, draw=FALSE),
name=name, vp=vp, cl="motif")
}
#' geom_motif
#'
#' geom_motif uses the locations of the four corners (xmin, xmax, ymin and
#' ymax) to plot motifs.
#'
#'
#' @param 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.
#' @param data The data to be displayed in this layer.
#' @param stat The statistical transformation to use on the data for this
#' layer, as a string.
#' @param position Position adjustment, either as a string, or the result of a
#' call to a position adjustment function.
#' @param \dots Other arguments passed on to layer().
#' @param ic.scale logical If TRUE, the height of each column is proportional
#' to its information content. Otherwise, all columns have the same height.
#' @param use.xy logical If TRUE, the required aesthethics will be x, y, width,
#' height, and motif. Otherwise, xmin, ymin, xmax, ymax and motif.
#' @param show.legend Not used.
#' @param inherit.aes If FALSE, overrides the default aesthetics, rather than
#' combining with them.
#' @return a layer that contains GeomMotif object.
#' @section Aesthetics: geom_motif() understands the following aesthetics
#' (required aesthetics are in bold): \itemize{ \item \strong{\code{xmin}}
#' \item \strong{\code{xmax}} \item \strong{\code{ymin}} \item
#' \strong{\code{ymax}} \item \strong{\code{motif}} \item \code{angle} \item
#' \code{fontfamily} \item \code{fontface} }
#'
#' OR
#'
#' \itemize{ \item \strong{\code{x}} \item \strong{\code{y}} \item
#' \strong{\code{width}} \item \strong{\code{height}} \item
#' \strong{\code{motif}} \item \code{angle} \item \code{fontfamily} \item
#' \code{fontface} }
#' @author Jianhong Ou
#' @export
#' @importFrom ggplot2 layer
#' @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$motif <- list(pcm2pfm(motif), pcm2pfm(motif))
#'
#' library(ggplot2)
#' ggplot(df, aes(xmin=xmin, ymin=ymin, xmax=xmax, ymax=ymax, motif=motif)) +
#' geom_motif() + theme_bw() + ylim(0, 1) + xlim(0, 1)
#'
geom_motif <- function(mapping = NULL, data = NULL,
stat = "identity", position = "identity",
...,
ic.scale=TRUE,
use.xy=FALSE,
show.legend = NA,
inherit.aes = TRUE) {
layer(
data = data,
mapping = mapping,
stat = stat,
geom = if(use.xy) GeomMotifA else GeomMotif,
position = position,
show.legend = show.legend,
inherit.aes = inherit.aes,
params = list(
ic.scale = ic.scale,
...
)
)
}
#' GeomMotif object
#'
#' GeomMotif object is a ggproto object.
#'
#'
#' @name GeomMotif
#' @format The format is: Classes 'GeoMotif', 'Geom', 'ggproto', 'gg' <ggproto
#' object: Class GeoMotif, Geom, gg> aesthetics: function default_aes: uneval
#' draw_group: function draw_key: function draw_layer: function draw_panel:
#' function extra_params: na.rm handle_na: function non_missing_aes:
#' optional_aes: parameters: function required_aes: xmin ymin xmax ymax motif
#' setup_data: function use_defaults: function super: <ggproto object: Class
#' Geom, gg>
#' @seealso geom_motif
#' @export
#' @importFrom ggplot2 ggproto aes Geom
#' @examples
#'
#' pcm <- read.table(file.path(find.package("motifStack"),
#' "extdata", "bin_SOLEXA.pcm"))
#' pcm <- pcm[,3:ncol(pcm)]
#' rownames(pcm) <- c("A","C","G","T")
#' motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")
#'
#' df <- data.frame(xmin=c(.25, .25), ymin=c(.25, .75), xmax=c(.75, .75), ymax=c(.5, 1))
#' df$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)
#'
#'
GeomMotif <-
ggproto("GeomMotif", Geom,
required_aes = c("xmin", "ymin", "xmax", "ymax", "motif"),
default_aes = aes(angle=0, fontfamily="sans",
fontface="bold"),
draw_panel = function(data, panel_params, coord, ic.scale=TRUE){
coords <- coord$transform(data, panel_params)
n <- nrow(coords)
do.call(gList, lapply(seq.int(n), function(.id){
motifGrob(pfm=coords$motif[[.id]],
x=mean(c(coords$xmin[.id], coords$xmax[.id])),
y=mean(c(coords$ymin[.id], coords$ymax[.id])),
width=coords$xmax[.id] - coords$xmin[.id],
height=coords$ymax[.id] - coords$ymin[.id],
angle=coords$angle[.id], ic.scale=ic.scale,
default.units = "native",
gp = gpar(fontfamily=coords$fontfamily[.id],
fontface=coords$fontface[.id]),
name = paste0("geom_motif_", .id))
}))
})
GeomMotifA <-
ggproto("GeomMotif", Geom,
required_aes = c("x", "y", "width", "height", "motif"),
default_aes = aes(angle=0, fontfamily="sans",
fontface="bold"),
draw_panel = function(data, panel_params, coord, ic.scale=TRUE){
if(is.unit(data$x)) data$x <- convertUnit(data$x, unitTo = "native", valueOnly = TRUE)
if(is.unit(data$y)) data$y <- convertUnit(data$x, unitTo = "native", valueOnly = TRUE)
if(is.unit(data$width)) data$width <- convertUnit(data$width, unitTo = "native", valueOnly = TRUE)
if(is.unit(data$height)) data$height <- convertUnit(data$height, unitTo = "native", valueOnly = TRUE)
hw <- data$width/2
hh <- data$height/2
data$xmin <- data$x - hw
data$ymin <- data$y - hh
data$xmax <- data$x + hw
data$ymax <- data$y + hh
coords <- coord$transform(data, panel_params)
n <- nrow(coords)
do.call(gList, lapply(seq.int(n), function(.id){
motifGrob(pfm=coords$motif[[.id]],
x=mean(c(coords$xmin[.id], coords$xmax[.id])),
y=mean(c(coords$ymin[.id], coords$ymax[.id])),
width=coords$xmax[.id] - coords$xmin[.id],
height=coords$ymax[.id] - coords$ymin[.id],
angle=coords$angle[.id], ic.scale=ic.scale,
default.units = "native",
gp = gpar(fontfamily=coords$fontfamily[.id],
fontface=coords$fontface[.id]),
name = paste0("geom_motif_", .id))
}))
})
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