---
title: "motifStack Vignette"
author: "Jianhong Ou, Lihua Julie Zhu"
date: "`r doc_date()`"
package: "`r pkg_ver('motifStack')`"
bibliography: ref.bib
abstract: >
  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.
vignette: >
  %\VignetteIndexEntry{motifStack Vignette}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
output:
  BiocStyle::html_document
---

# Introduction
A sequence logo, based on information theory, has been widely used as a graphical 
representation of sequence conservation (aka motif) in multiple amino acid or 
nucleic acid sequences. Sequence motif represents conserved characteristics 
such as DNA binding sites, where transcription factors bind, and catalytic sites 
in enzymes. Although many tools, such as seqlogo\cite{Oliver2006}, have been 
developed to create sequence motif and to represent it as individual sequence 
logo, software tools for depicting the relationship among multiple sequence 
motifs are still lacking. We developed a flexible and powerful open-source 
R/Bioconductor package, motifStack, for visualization of the alignment of 
multiple sequence motifs.

# Prepare environment
You will need ghostscript: the full path to the executable can be set by the environment variable R\_GSCMD. 
If this is unset, a GhostScript executable will be searched by name on your path. For example, on a Unix, linux or Mac "gs" is used for searching, 
and on Windows the setting of the environment variable GSC is used, otherwise commands "gswi64c.exe" then "gswin32c.exe" are tried.

Example on Windows: assume that the gswin32c.exe is installed at C:\\ Program Files\\ gs\\ gs9.06\\ bin, then open R and try:
```{r setup, eval=FALSE, echo=TRUE}
Sys.setenv(R_GSCMD=file.path("C:", "Program Files", "gs", 
                             "gs9.06", "bin", "gswin32c.exe"))
```

# Examples of using motifStack
## plot a DNA sequence logo with different fonts and colors
Users can select different fonts and colors to draw the sequence logo.
```{r 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)
```

## 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".

```{r 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)
```

## 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.
```{r 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)
```

## 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\cite{Eloi2010}::motifDistances, 
which implemented STAMP\cite{Mahony2007}. 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.

```{r 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)
```

```{r 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")
```

```{r 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)
```

## plot a sequence logo cloud
We can also plot a sequence logo cloud for DNA sequence logo.

```{r 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)
```

## plot grouped sequence logo
To plot grouped sequence logo, except do motifCloud, we can also plot it with radialPhylog style.

```{r 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
We can also plot it with circos style. In circos style,
we can plot two group of motifs and with multiple color rings.

```{r 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
We can also plot it with pile style. In pile style,
we can plot two group of motifs and with multiple color annoations.

```{r 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)
```

# docker container for motifStack}
\href{https://docs.docker.com/}{Docker} allows software to be packaged into containers and the containers can be run any platform as well using a virtual machine called boot2docker. motifStack has its docker image stored in \href{https://hub.docker.com/r/jianhong/motifstack_1.13.6/}{Docker Hub}. Users can download the image and run.

<pre>
docker pull jianhong/motifstack_1.13.6
cd ~ ## in windows, please try cd c:\\ Users\\ username
mkdir tmp4motifstack ## this will be the share folder for your host and container.
docker run -ti --rm -v ${PWD}/tmp4motifstack:/volume/data jianhong/motifstack_1.13.6 R
## in R
setwd("/tmp")
library(motifStack)
packageVersion("motifStack")
pcmpath <- "pcmsDatasetFly"
pcms <- readPCM(pcmpath)
pfms <- lapply(pcms, pcm2pfm)
matalign_path <- "/usr/bin/matalign"
neighbor_path <- "/usr/bin/phylip/neighbor"
outpath <- "output"
system(paste("perl MatAlign2tree.pl --in . --pcmpath", pcmpath, "--out", outpath,
    "--matalign", matalign_path, "--neighbor", neighbor_path, "--tree","UPGMA"))
newickstrUPGMA <- readLines(con=file.path(outpath, "NJ.matalign.distMX.nwk"))
phylog <- newick2phylog(newickstrUPGMA, FALSE)
leaves <- names(phylog$leaves)
motifs <- pfms[leaves]
motifSig <- motifSignature(motifs, phylog, groupDistance=2, min.freq=1, trim=.2)
sig <- signatures(motifSig)
gpCol <- sigColor(motifSig)
leaveNames <- gsub("^Dm_", "", leaves)
pdf("/volume/data/test.pdf", width=8, height=11)
motifPiles(phylog=phylog, DNAmotifAlignment(motifs), sig, 
    col.pfms=gpCol, col.pfms.width=.01, 
    col.pfms2=gpCol, col.pfms2.width=.01, 
    labels.leaves=leaveNames, 
    plotIndex=c(FALSE, TRUE), IndexCex=1, 
    groupDistance=2, clabel.leaves=1)
dev.off()
</pre>

You will see the test.pdf file in the folder of tmp4motifstack. 

# Session Info
```{r sessionInfo}
sessionInfo()
```