Nothing
########################################
### Echelon dendrogram with clusters ###
########################################
e.cluster.dendrogram <- function(echelon.obj,n.sim,cluster.legend.pos,cluster_reg,p_rank,para){
if(!is.null(echelon.obj$coord) && length(para) == 0){
x <- echelon.obj$x
coord <- echelon.obj$coord
locs <- echelon.obj$locs
x_pos <- echelon.obj$x_pos
separates <- echelon.obj$separates
replayPlot(echelon.obj$current.dendrogram)
}
else{
main <- ifelse(length(para$main)==0, numeric(0), para$main)
ylab <- ifelse(length(para$ylab)==0, numeric(0), para$ylab)
yaxes <- ifelse(length(para$yaxes)==0, TRUE, para$yaxes)
if(length(para$ylim)==0) ylim <- NULL
else ylim <- para$ylim
xaxes <- ifelse(length(para$xaxes)==0, FALSE, para$xaxes)
if(length(para$xdper)==0) xdper <- c(0,1)
else xdper <- para$xdper
if(length(para$dmai)==0) dmai <- NULL
else dmai <- para$dmai
lwd <- ifelse(length(para$lwd)==0, 1, para$lwd)
symbols <- ifelse(length(para$symbols)==0, 4, para$symbols)
cex.symbols <- ifelse(length(para$cex.symbols)==0, 0.5, para$cex.symbols)
col2 <- ifelse(length(para$col.symbols)==0, 4, para$col.symbols)
ens <- ifelse(length(para$ens)==0, TRUE, para$ens)
adj.ens <- ifelse(length(para$adj.ens)==0, 1, para$adj.ens)
cex.ens <- ifelse(length(para$cex.ens)==0, 0.8, para$cex.ens)
col3 <- ifelse(length(para$col.ens)==0, 1, para$col.ens)
col1 <- ifelse(length(para$col)==0, 1, para$col)
peaks <- echelon.obj$peaks
locs <- echelon.obj$locs
x <- echelon.obj$x
separates <- echelon.obj$separates
c_separates <- echelon.obj$c_separates
number <- echelon.obj$number
parents <- echelon.obj$parents
pare_locs <- echelon.obj$pare_locs
progeny <- echelon.obj$progeny
e.dendrogram.axis(main,ylab,yaxes,ylim,xaxes,xdper,dmai,peaks,x)
temp <- e.dendrogram(peaks,locs,x,separates,c_separates,number,parents,
pare_locs,progeny,symbols,col.symbols=col2,cex.symbols,
lwd,col=col1,ens,adj.ens,col.ens=col3,cex.ens,limb=FALSE)
coord <- temp$coordinate
x_pos <- temp$x_pos
}
if(nrow(cluster_reg) <= 5) l <- nrow(cluster_reg)
else l <- 5
cluster.col <- c(2:6)
leg.txt <- NULL
leg.col <- NULL
for(j in 1:l){
k <- NULL
k2 <- NULL
for(i in 1:length(separates)) k <- c(k,rep(x_pos[i],times=separates[i]))
temp <- cluster_reg[j,][!is.na(cluster_reg[j,])]
for(i in 1:length(temp)) k2 <- c(k2,which(temp[i] == locs))
points(k[k2],x[locs][k2],pch=10,cex=1.5,col=cluster.col[j])
if(!is.null(p_rank)) leg.txt <- c(leg.txt,paste(j,"- p-value:",p_rank[j]/(n.sim+1)))
else leg.txt <- c(leg.txt,paste(j,"- p-value:---"))
leg.col <- c(leg.col,cluster.col[j])
}
legend(cluster.legend.pos,legend=leg.txt,text.col=leg.col)
list(coord = coord,regions.value=x[locs])
}
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