## ----checkplatform, include=FALSE---------------------------------------------
library(knitr)
library(motifStack)
library(MotifDb)
library(ade4)
library(ggplot2)
library(TFBSTools)
library(JASPAR2020)
if(.Platform$OS.type=="windows"){
  opts_chunk$set(eval=FALSE)
}

## ----importMatrix,fig.cap="import data from PFMatrixList",fig.width=6,fig.height=3----
# library(motifStack)
# library(JASPAR2020)
# motifs <- importMatrix(getMatrixSet(JASPAR2020,
#                                     list(species="Mus musculus")))
# plot(motifs[[1]])

## ----importFromFiles,fig.cap="import data from file",fig.width=6,fig.height=3----
# RUNX1 <- importMatrix(system.file("extdata", "MA0002.1.jaspar",
#                                   package = "motifStack",
#                                   mustWork = TRUE))[[1]]
# plot(RUNX1)

## ----DNAseqLogo,fig.cap="Plot a DNA sequence logo with different fonts and colors",fig.width=8,fig.height=2.5----
# 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")
# plot(motif)
# #plot the logo with same height
# plot(motif, ic.scale=FALSE, ylab="probability")
# #try a different font and a different color group
# motif@color <- colorset(colorScheme='basepairing')
# plot(motif,font="serif")

## ----seqLogoMarkers, fig.cap="Plot a DNA sequence logo with markers", fig.width=8,fig.height=2.5----
# markerRect <- new("marker", type="rect", start=6, stop=7, gp=gpar(lty=2, fill=NA, col="orange"))
# markerLine <- new("marker", type="line", start=2, stop=7, gp=gpar(lwd=2, col="red"))
# markerText <- new("marker", type="text", start=c(1, 5),
#                   label=c("*", "core"), gp=gpar(cex=2, col="red"))
# motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA",
#              markers=c(markerRect, markerLine, markerText))
# plot(motif)

## ----seqLogoXaxis, fig.cap="Plot a DNA sequence logo with pre-defined xlabels", fig.width=8,fig.height=2.5----
# plot(motif, xaxis=paste0("pos", seq.int(7)+10))

## ----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)

## ----affinityLogo,fig.cap="Plot an affinity logo",fig.width=6,fig.height=3----
# library(motifStack)
# motif<-matrix(
#   c(
#     .846, .631, .593, .000, .000, .000, .434, .410, 1.00, .655, .284, .000, .000, .771, .640, .961,
#     .625, .679, .773, 1.00, 1.00, .000, .573, .238, .397, 1.00, 1.00, .000, .298, 1.00, 1.00, .996,
#     1.00, 1.00, 1.00, .228, .000, 1.00, 1.00, .597, .622, .630, .000, 1.00, 1.00, .871, .617, 1.00,
#     .701, .513, .658, .000, .000, .247, .542, 1.00, .718, .686, .000, .000, .000, .595, .437, .970
#   ), nrow=4, byrow = TRUE)
# rownames(motif) <- c("A", "C", "G", "T")
# motif<-new("psam", mat=motif, name="affinity logo",
#            markers=list(new("marker", type="rect",
#                             start=c(4, 11), stop=c(6, 13),
#                             gp=gpar(col="#009E73", fill=NA, lty=2))))
# plot(motif)

## ----logostack,fig.cap="Plot motifs with sequence logo stack style",fig.width=4,fig.height=6----
# library(motifStack)
# #####Input#####
# motifs<-importMatrix(dir(file.path(find.package("motifStack"),
#                                    "extdata"),"pcm$",
#                          full.names = TRUE))
# 
# ## plot stacks
# motifStack(motifs, layout="stack", ncex=1.0)

## ----rnalogostack,fig.cap="Plot RNA motifs with sequence logo stack style", fig.width=4,fig.height=6----
# rnaMotifs <- DNAmotifToRNAmotif(motifs)
# names(rnaMotifs)
# motifStack(rnaMotifs, layout = "stack",
#            reorder=FALSE) ## we can also use reorder=FALSE to keep the order of input.

## ----logostack2,fig.cap="Plot affinity logos with sequence logo stack style",fig.width=4,fig.height=3.5----
# motif2 <- motif
# motif2$mat <- motif$mat[, 5:12]
# motif2$name <- "logo2"
# psamMotifs <- list(motif, motif2)
# motifStack(psamMotifs)

## ----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, 30)
# ## creat a list of object of pfm
# motifs2 <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
#   new("pfm",mat=.ele, name=.name)}, SIMPLIFY = FALSE)
# ## trim the motifs
# motifs2 <- lapply(motifs2, trimMotif, t=0.4)
# ## setting colors
# library(RColorBrewer)
# color <- brewer.pal(10, "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=3), col.bg.alpha=0.3,
#            col.leaves=rep(color, each=3),
#            col.inner.label.circle=rep(color, each=3),
#            inner.label.circle.width=0.05,
#            col.outer.label.circle=rep(color, each=3),
#            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="")
# ## create a list of pfm objects
# pfms <- mapply(names(pfms), pfms, FUN=function(.ele, .pfm){
#   new("pfm",mat=.pfm, name=.ele)}
#                ,SIMPLIFY = FALSE)
# ## use matalign to calculate the distances of motifs
# hc <- clusterMotifs(pfms)
# ## convert the hclust to phylog object
# library(ade4)
# phylog <- ade4::hclust2phylog(hc)
# ## reorder the pfms by the order of hclust
# leaves <- names(phylog$leaves)
# pfms <- pfms[leaves]
# ## extract the motif signatures
# motifSig <- motifSignature(pfms, phylog, cutoffPval=0.0001, 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=3), col.bg.alpha=0.3,
#                               col.leaves=rep(rev(color), each=3),
#                               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 cirsoc 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(), 30),
#                            sample(colors(), 30),
#                            sample(colors(), 30)),
#             angle=350, motifScale="logarithmic")

## ----motifPilesHeatmap,fig.cap="Grouped sequence logo with a heatmap",fig.width=6,fig.height=6----
# ## plot the logo stack with heatmap.
# df <- data.frame(A=runif(n = 30), B=runif(n = 30), C=runif(n = 30), D=runif(n = 30))
# map2col <- function(x, pal){
#   rg <- range(x)
#   pal[findInterval(x, seq(rg[1], rg[2], length.out = length(pal)+1),
#                    all.inside = TRUE)]
# }
# dl <- lapply(df, map2col, pal=heat.colors(10))
# ## alignment of the pfms, this step will make the motif logos occupy
# ## more space. Users can skip this alignment to see the difference.
# pfmsAligned <- DNAmotifAlignment(pfms)
# ## plot motifs
# motifPiles(phylog=phylog, pfms=pfmsAligned,
#             col.tree=rep(color, each=5),
#             col.leaves=rep(rev(color), each=5),
#             col.pfms2=gpCol,
#             r.anno=rep(0.02, length(dl)),
#             col.anno=dl,
#             motifScale="logarithmic",
#             plotIndex=TRUE,
#             groupDistance=10)

## ----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)

## ----geommotif,fig.width=8, fig.height=8--------------------------------------
# pcm <- read.table(file.path(find.package("motifStack"),
#                             "extdata", "bin_SOLEXA.pcm"))
# pcm <- pcm[,3:ncol(pcm)]
# rownames(pcm) <- c("A","C","G","T")
# markerRect <- new("marker", type="rect", start=6, stop=7, gp=gpar(lty=2, fill=NA, col="orange"))
# markerLine <- new("marker", type="line", start=3, stop=5, gp=gpar(lwd=2, col="red"))
# markerText <- new("marker", type="text", start=1, label="*", gp=gpar(cex=2, col="red"))
# motif <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA",
#              markers=c(markerRect, markerLine, markerText))
# pfm <- pcm2pfm(motif)
# df <- data.frame(xmin=c(.25, .25), ymin=c(.25, .75), xmax=c(.75, .75), ymax=c(.5, 1),
#                  fontfamily=c("serif", "mono"), fontface=c(2, 1))
# df$motif <- list(pfm, pfm)
# 
# library(ggplot2)
# 
# ggplot(df, aes(xmin=xmin, ymin=ymin, xmax=xmax, ymax=ymax, motif=motif,
#                fontfamily=fontfamily, fontface=fontface)) +
#     geom_motif() + theme_bw() + ylim(0, 1) + xlim(0, 1)
# 
# df <- data.frame(x=.5, y=c(.25, .75), width=.5, height=.25,
#                  fontfamily=c("serif", "mono"), fontface=c(2, 1))
# df$motif <- list(pfm, pfm)
# 
# ggplot(df, aes(x=x, y=y, width=width, height=height, motif=motif,
#                fontfamily=fontfamily, fontface=fontface)) +
#     geom_motif(use.xy=TRUE) + theme_bw() + ylim(0, 1) + xlim(0, 1)

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

