######################
##
## plot sequence logo
## ######################
letterA <- function(x.pos,y.pos,ht,wt,id=NULL){
x <- c(0,4,6,10,8,6.8,3.2,2,0,3.6,5,6.4,3.6)
y <- c(0,10,10,0,0,3,3,0,0,4,7.5,4,4)
x <- 0.1*x
y <- 0.1*y
x <- x.pos + wt*x
y <- y.pos + ht*y
if (is.null(id)){
id <- c(rep(1,9),rep(2,4))
}else{
id <- c(rep(id,9),rep(id+1,4))
}
fill <- c("#E41A1C","white")
list(x=x,y=y,id=id,fill=fill)
}
## T
letterT <- function(x.pos,y.pos,ht,wt,id=NULL){
x <- c(0,10,10,6,6,4,4,0)
y <- c(10,10,9,9,0,0,9,9)
x <- 0.1*x
y <- 0.1*y
x <- x.pos + wt*x
y <- y.pos + ht*y
if (is.null(id)){
id <- rep(1,8)
}else{
id <- rep(id,8)
}
fill <- "#4DAF4A"
list(x=x,y=y,id=id,fill=fill)
}
## C
letterC <- function(x.pos,y.pos,ht,wt,id=NULL){
angle1 <- seq(0.3+pi/2,pi,length=100)
angle2 <- seq(pi,1.5*pi,length=100)
x.l1 <- 0.5 + 0.5*sin(angle1)
y.l1 <- 0.5 + 0.5*cos(angle1)
x.l2 <- 0.5 + 0.5*sin(angle2)
y.l2 <- 0.5 + 0.5*cos(angle2)
x.l <- c(x.l1,x.l2)
y.l <- c(y.l1,y.l2)
x <- c(x.l,rev(x.l))
y <- c(y.l,1-rev(y.l))
x.i1 <- 0.5 +0.35*sin(angle1)
y.i1 <- 0.5 +0.35*cos(angle1)
x.i1 <- x.i1[y.i1<=max(y.l1)]
y.i1 <- y.i1[y.i1<=max(y.l1)]
y.i1[1] <- max(y.l1)
x.i2 <- 0.5 +0.35*sin(angle2)
y.i2 <- 0.5 +0.35*cos(angle2)
x.i <- c(x.i1,x.i2)
y.i <- c(y.i1,y.i2)
x1 <- c(x.i,rev(x.i))
y1 <- c(y.i,1-rev(y.i))
x <- c(x,rev(x1))
y <- c(y,rev(y1))
x <- x.pos + wt*x
y <- y.pos + ht*y
if (is.null(id)){
id <- rep(1,length(x))
}else{
id <- rep(id,length(x))
}
fill <- "#377EB8"
list(x=x,y=y,id=id,fill=fill)
}
## G
letterG <- function(x.pos,y.pos,ht,wt,id=NULL){
angle1 <- seq(0.3+pi/2,pi,length=100)
angle2 <- seq(pi,1.5*pi,length=100)
x.l1 <- 0.5 + 0.5*sin(angle1)
y.l1 <- 0.5 + 0.5*cos(angle1)
x.l2 <- 0.5 + 0.5*sin(angle2)
y.l2 <- 0.5 + 0.5*cos(angle2)
x.l <- c(x.l1,x.l2)
y.l <- c(y.l1,y.l2)
x <- c(x.l,rev(x.l))
y <- c(y.l,1-rev(y.l))
x.i1 <- 0.5 +0.35*sin(angle1)
y.i1 <- 0.5 +0.35*cos(angle1)
x.i1 <- x.i1[y.i1<=max(y.l1)]
y.i1 <- y.i1[y.i1<=max(y.l1)]
y.i1[1] <- max(y.l1)
x.i2 <- 0.5 +0.35*sin(angle2)
y.i2 <- 0.5 +0.35*cos(angle2)
x.i <- c(x.i1,x.i2)
y.i <- c(y.i1,y.i2)
x1 <- c(x.i,rev(x.i))
y1 <- c(y.i,1-rev(y.i))
x <- c(x,rev(x1))
y <- c(y,rev(y1))
h1 <- max(y.l1)
r1 <- max(x.l1)
h1 <- 0.4
x.add <- c(r1,0.5,0.5,r1-0.2,r1-0.2,r1,r1)
y.add <- c(h1,h1,h1-0.1,h1-0.1,0,0,h1)
if (is.null(id)){
id <- c(rep(1,length(x)),rep(2,length(x.add)))
}else{
id <- c(rep(id,length(x)),rep(id+1,length(x.add)))
}
x <- c(rev(x),x.add)
y <- c(rev(y),y.add)
x <- x.pos + wt*x
y <- y.pos + ht*y
fill <- c("#F0E442","#F0E442")
list(x=x,y=y,id=id,fill=fill)
}
addLetter <- function(letters,which,x.pos,y.pos,ht,wt){
if (which == "A"){
letter <- letterA(x.pos,y.pos,ht,wt)
}else if (which == "C"){
letter <- letterC(x.pos,y.pos,ht,wt)
}else if (which == "G"){
letter <- letterG(x.pos,y.pos,ht,wt)
}else if (which == "T"){
letter <- letterT(x.pos,y.pos,ht,wt)
}else{
stop("which must be one of A,C,G,T")
}
letters$x <- c(letters$x,letter$x)
letters$y <- c(letters$y,letter$y)
lastID <- ifelse(is.null(letters$id),0,max(letters$id))
letters$id <- c(letters$id,lastID+letter$id)
letters$fill <- c(letters$fill,letter$fill)
letters
}
## plot a sequence logo
seqLogo <- function(pwm, ic.scale=TRUE, xaxis=TRUE, yaxis=TRUE, xfontsize=15, yfontsize=15){
if (class(pwm) == "pwm"){
pwm <- pwm@pwm
}else if (class(pwm) == "data.frame"){
pwm <- as.matrix(pwm)
}else if (class(pwm) != "matrix"){
stop("pwm must be of class matrix or data.frame")
}
if (any(abs(1 - apply(pwm,2,sum)) > 0.01))
stop("Columns of PWM must add up to 1.0")
chars <- c("A","C","G","T")
letters <- list(x=NULL,y=NULL,id=NULL,fill=NULL)
npos <- ncol(pwm)
if (ic.scale){
ylim <- 2
ylab <- "Information content"
facs <- pwm2ic(pwm)
}else{
ylim <- 1
ylab <- "Probability"
facs <- rep(1, npos)
}
wt <- 1
x.pos <- 0
for (j in 1:npos){
column <- pwm[,j]
hts <- 0.95*column*facs[j]
letterOrder <- order(hts)
y.pos <- 0
for (i in 1:4){
letter <- chars[letterOrder[i]]
ht <- hts[letterOrder[i]]
if (ht>0) letters <- addLetter(letters,letter,x.pos,y.pos,ht,wt)
y.pos <- y.pos + ht + 0.01
}
x.pos <- x.pos + wt
}
grid.newpage()
bottomMargin = ifelse(xaxis, 2 + xfontsize/3.5, 2)
leftMargin = ifelse(yaxis, 2 + yfontsize/3.5, 2)
pushViewport(plotViewport(c(bottomMargin,leftMargin,2,2)))
pushViewport(dataViewport(0:ncol(pwm),0:ylim,name="vp1"))
grid.polygon(x=unit(letters$x,"native"), y=unit(letters$y,"native"),
id=letters$id,
gp=gpar(fill=letters$fill,col="transparent"))
if (xaxis){
grid.xaxis(at=seq(0.5,ncol(pwm)-0.5),label=1:ncol(pwm), gp=gpar(fontsize=xfontsize))
grid.text("Position",y=unit(-3,"lines"), gp=gpar(fontsize=xfontsize))
}
if (yaxis){
grid.yaxis(gp=gpar(fontsize=yfontsize))
grid.text(ylab,x=unit(-3,"lines"),rot=90, gp=gpar(fontsize=yfontsize))
}
popViewport()
popViewport()
par(ask=FALSE)
}
## plot a complementary sequence logo
seqLogoRev <- function(pwm, ic.scale=TRUE, xaxis=TRUE, yaxis=TRUE, xfontsize=15, yfontsize=15){
if (class(pwm) == "pwm"){
pwm <- pwm@pwm
}else if (class(pwm) == "data.frame"){
pwm <- as.matrix(pwm)
}else if (class(pwm) != "matrix"){
stop("pwm must be of class matrix or data.frame")
}
if (any(abs(1 - apply(pwm,2,sum)) > 0.01))
stop("Columns of PWM must add up to 1.0")
chars <- c("T","G","C","A")
letters <- list(x=NULL,y=NULL,id=NULL,fill=NULL)
npos <- ncol(pwm)
if (ic.scale){
ylim <- 2
ylab <- "Information content"
facs <- pwm2ic(pwm)
}else{
ylim <- 1
ylab <- "Probability"
facs <- rep(1, npos)
}
wt <- 1
x.pos <- 0
for (j in 1:npos){
column <- pwm[,j]
hts <- 0.95*column*facs[j]
letterOrder <- order(hts)
y.pos <- 0
for (i in 1:4){
letter <- chars[letterOrder[i]]
ht <- hts[letterOrder[i]]
if (ht>0) letters <- addLetter(letters,letter,x.pos,y.pos,ht,wt)
y.pos <- y.pos + ht + 0.01
}
x.pos <- x.pos + wt
}
grid.newpage()
bottomMargin = ifelse(xaxis, 2 + xfontsize/3.5, 2)
leftMargin = ifelse(yaxis, 2 + yfontsize/3.5, 2)
pushViewport(plotViewport(c(bottomMargin,leftMargin,2,2)))
pushViewport(dataViewport(0:ncol(pwm),0:ylim,name="vp1"))
grid.polygon(x=unit(letters$x,"native"), y=unit(letters$y,"native"),
id=letters$id,
gp=gpar(fill=letters$fill,col="transparent"))
if (xaxis){
grid.xaxis(at=seq(0.5,ncol(pwm)-0.5),label=1:ncol(pwm), gp=gpar(fontsize=xfontsize))
grid.text("Position",y=unit(-3,"lines"), gp=gpar(fontsize=xfontsize))
}
if (yaxis){
grid.yaxis(gp=gpar(fontsize=yfontsize))
grid.text(ylab,x=unit(-3,"lines"),rot=90, gp=gpar(fontsize=yfontsize))
}
popViewport()
popViewport()
par(ask=FALSE)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.