## ----setup, eval=FALSE, echo=TRUE----------------------------------------
#  Sys.setenv(R_GSCMD=file.path("C:", "Program Files", "gs",
#                               "gs9.06", "bin", "gswin32c.exe"))

## ----DNAseqLogo,fig.cap="Plot a DNA sequence logo with different fonts and colors",fig.width=8,fig.height=6----
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)

## ----RNAseqLogo,fig.cap="Plot an RNA sequence logo",fig.width=6,fig.height=3----
rna <- pcm
rownames(rna)[4] <- "U"
motif <- new("pcm", mat=as.matrix(rna), name="RNA_motif")
plot(motif)

## ----AAseqLogo,fig.cap="Plot an sequence logo with any symbols as you want such as amino acid sequence logo",fig.width=6,fig.height=3----
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)

## ----logostack,fig.cap="Plot motifs with sequence logo stack style",fig.width=4,fig.height=6----
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)

## ----treestack,fig.cap="Sequence logo stack with hierarchical cluster tree",fig.width=5,fig.height=6----
## plot stacks with hierarchical tree
#motifStack(motifs, layout="tree")

## ----radialstack,fig.cap="Plot motifs in a radial style when the number of motifs is too much to be shown in a vertical stack",fig.width=6,fig.height=6----
## 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")
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)

## ----motifCloud,fig.cap="Sequence logo cloud with rectangle packing layout",fig.width=6,fig.height=6----
## 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)

## ----motifRadialPhylog,fig.cap="Grouped sequence logo with radialPhylog style layout",fig.width=6,fig.height=6----
## 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")

## ----motifCircos,fig.cap="Grouped sequence logo with circos style layout",fig.width=6,fig.height=6----
## 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")

## ----motifPiles,fig.cap="Grouped sequence logo with piles style layout",fig.width=6,fig.height=6----
## 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)

## ----browseMotifs,fig.width=8,fig.height=8-------------------------------
browseMotifs(pfms = pfms, phylog = phylog, layout="tree", yaxis = FALSE, baseWidth=6, baseHeight = 15)

## ----browseMotifsRadialPhylog,fig.width=8,fig.height=8-------------------
browseMotifs(pfms = pfms, phylog = phylog, layout="radialPhylog", yaxis = FALSE, xaxis = FALSE, baseWidth=6, baseHeight = 15)

## ----sessionInfo---------------------------------------------------------
sessionInfo()

