3 Examples of using motifStack
3.1 plot a DNA sequence logo with different fonts and colors
Users can select different fonts and colors to draw the sequence logo.
suppressPackageStartupMessages(library(motifStack))
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")
##pfm object
#motif <- pcm2pfm(pcm)
#motif <- new("pfm", mat=motif, name="bin_SOLEXA")
opar<-par(mfrow=c(4,1))
plot(motif)
#plot the logo with same height
plot(motif, ic.scale=FALSE, ylab="probability")
#try a different font
plot(motif, font="mono,Courier")
#try a different font and a different color group
motif@color <- colorset(colorScheme='basepairing')
plot(motif,font="Times")
par(opar)3.2 plot a RNA sequence logo
From DNA sequence logo to RNA sequence logo, you just need to change the rowname of the matrix from “T” to “U”.
rna <- pcm
rownames(rna)[4] <- "U"
motif <- new("pcm", mat=as.matrix(rna), name="RNA_motif")
plot(motif)
3.3 plot an amino acid sequence logo
Given that motifStack allows to use any letters as symbols, it can also be used to draw amino acid sequence logos.
library(motifStack)
protein<-read.table(file.path(find.package("motifStack"),"extdata","cap.txt"))
protein<-t(protein[,1:20])
motif<-pcm2pfm(protein)
motif<-new("pfm", mat=motif, name="CAP",
color=colorset(alphabet="AA",colorScheme="chemistry"))
plot(motif)
3.4 plot sequence logo stack
motifStack is designed to show multiple motifs in same canvas. To show the sequence logo stack, the distance of motifs need to be calculated first for example by using MotIV::motifDistances, which implemented STAMP. After alignment, users can use plotMotifLogoStack function to draw sequence logos stack or use plotMotifLogoStackWithTree function to show the distance tree with the sequence logos stack or use plotMotifStackWithRadialPhylog function to plot sequence logo stack in radial style in the same canvas. There is a shortcut function named as motifStack. Use stack layout to call plotMotifLogoStack, treeview layout to call plotMotifLogoStackWithTree and radialPhylog to call plotMotifStackWithRadialPhylog.
suppressPackageStartupMessages(library(motifStack))
#####Input#####
pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
motifs<-lapply(pcms,pcm2pfm)
## plot stacks
#motifStack(motifs, layout="stack", ncex=1.0)## plot stacks with hierarchical tree
#motifStack(motifs, layout="tree")## When the number of motifs is too much to be shown in a vertical stack,
## motifStack can draw them in a radial style.
## random sample from MotifDb
library("MotifDb")## See system.file("LICENSE", package="MotifDb") for use restrictions.matrix.fly <- query(MotifDb, "Dmelanogaster")
motifs2 <- as.list(matrix.fly)
## use data from FlyFactorSurvey
motifs2 <- motifs2[grepl("Dmelanogaster\\-FlyFactorSurvey\\-",
names(motifs2))]
## format the names
names(motifs2) <- gsub("Dmelanogaster_FlyFactorSurvey_", "",
gsub("_FBgn\\d+$", "",
gsub("[^a-zA-Z0-9]","_",
gsub("(_\\d+)+$", "", names(motifs2)))))
motifs2 <- motifs2[unique(names(motifs2))]
pfms <- sample(motifs2, 50)
## creat a list of object of pfm
motifs2 <- lapply(names(pfms),
function(.ele, pfms){new("pfm",mat=pfms[[.ele]], name=.ele)}
,pfms)
## trim the motifs
motifs2 <- lapply(motifs2, trimMotif, t=0.4)
## setting colors
library(RColorBrewer)
color <- brewer.pal(12, "Set3")
## plot logo stack with radial style
motifStack(motifs2, layout="radialPhylog",
circle=0.3, cleaves = 0.2,
clabel.leaves = 0.5,
col.bg=rep(color, each=5), col.bg.alpha=0.3,
col.leaves=rep(color, each=5),
col.inner.label.circle=rep(color, each=5),
inner.label.circle.width=0.05,
col.outer.label.circle=rep(color, each=5),
outer.label.circle.width=0.02,
circle.motif=1.2,
angle=350)
3.5 plot a sequence logo cloud
We can also plot a sequence logo cloud for DNA sequence logo.
## assign groups for motifs
groups <- rep(paste("group",1:5,sep=""), each=10)
names(groups) <- names(pfms)
## assign group colors
group.col <- brewer.pal(5, "Set3")
names(group.col)<-paste("group",1:5,sep="")
## use MotIV to calculate the distances of motifs
jaspar.scores <- MotIV::readDBScores(file.path(find.package("MotIV"),
"extdata",
"jaspar2010_PCC_SWU.scores"))
d <- MotIV::motifDistances(lapply(pfms, pfm2pwm))
hc <- MotIV::motifHclust(d, method="average")
## convert the hclust to phylog object
phylog <- hclust2phylog(hc)
## reorder the pfms by the order of hclust
leaves <- names(phylog$leaves)
pfms <- pfms[leaves]
## create a list of pfm objects
pfms <- lapply(names(pfms), function(.ele, pfms){
new("pfm",mat=pfms[[.ele]], name=.ele)}
,pfms)
## extract the motif signatures
motifSig <- motifSignature(pfms, phylog, groupDistance=0.01, min.freq=1)
## draw the motifs with a tag-cloud style.
motifCloud(motifSig, scale=c(6, .5),
layout="rectangles",
group.col=group.col,
groups=groups,
draw.legend=TRUE)
3.6 plot grouped sequence logo
To plot grouped sequence logo, except do motifCloud, we can also plot it with radialPhylog style.
## get the signatures from object of motifSignature
sig <- signatures(motifSig)
## set the inner-circle color for each signature
gpCol <- sigColor(motifSig)
## plot the logo stack with radial style.
plotMotifStackWithRadialPhylog(phylog=phylog, pfms=sig,
circle=0.4, cleaves = 0.3,
clabel.leaves = 0.5,
col.bg=rep(color, each=5), col.bg.alpha=0.3,
col.leaves=rep(rev(color), each=5),
col.inner.label.circle=gpCol,
inner.label.circle.width=0.03,
angle=350, circle.motif=1.2,
motifScale="logarithmic")
3.7 motifCircos
We can also plot it with circos style. In circos style, we can plot two group of motifs and with multiple color rings.
## plot the logo stack with radial style.
motifCircos(phylog=phylog, pfms=pfms, pfms2=sig,
col.tree.bg=rep(color, each=5), col.tree.bg.alpha=0.3,
col.leaves=rep(rev(color), each=5),
col.inner.label.circle=gpCol,
inner.label.circle.width=0.03,
col.outer.label.circle=gpCol,
outer.label.circle.width=0.03,
r.rings=c(0.02, 0.03, 0.04),
col.rings=list(sample(colors(), 50),
sample(colors(), 50),
sample(colors(), 50)),
angle=350, motifScale="logarithmic")
3.8 motifPiles
We can also plot it with pile style. In pile style, we can plot two group of motifs and with multiple color annoations.
## plot the logo stack with radial style.
motifPiles(phylog=phylog, pfms=pfms, pfms2=sig,
col.tree=rep(color, each=5),
col.leaves=rep(rev(color), each=5),
col.pfms2=gpCol,
r.anno=c(0.02, 0.03, 0.04),
col.anno=list(sample(colors(), 50),
sample(colors(), 50),
sample(colors(), 50)),
motifScale="logarithmic",
plotIndex=TRUE,
groupDistance=0.01)