##' return a data.frame that contains position information

 ##' for labeling column names of heatmap produced by `gheatmap` function
 ##'

 ##'

 ##' @title get_heatmap_column_position
 ##' @param treeview output of `gheatmap`
 ##' @param by one of 'bottom' or 'top'
 ##' @return data.frame
 ##' @export
 ##' @author Guangchuang Yu
 get_heatmap_column_position <- function(treeview, by="bottom") {
     by %<>% match.arg(c("bottom", "top"))
 
     mapping <- attr(treeview, "mapping")
     if (is.null(mapping)) {
         stop("treeview is not an output of `gheatmap`...")
     }
 
     colnames(mapping) <- c("label", "x")
     if (by == "bottom") {
         mapping$y <- 0
     } else {
         mapping$y <- max(treeview$data$y) + 1
     }
     return(mapping)
 }
 
 ##' scale x for tree with heatmap
 ##'

 ##'

 ##' @title scale_x_ggtree
 ##' @param tree_view tree view
 ##' @param breaks breaks for tree
 ##' @param labels lables for corresponding breaks
 ##' @return tree view
 ##' @importFrom ggplot2 scale_x_continuous
 ##' @importFrom ggplot2 scale_x_date
 ##' @export
 ##' @author Guangchuang Yu
 scale_x_ggtree <- function(tree_view, breaks=NULL, labels=NULL) {
     p <- get_tree_view(tree_view)
 
     mrsd <- get("mrsd", envir=tree_view$plot_env)
     if (!is.null(mrsd) && class(p$data$x) == "Date") {
         x <- Date2decimal(p$data$x)
     } else {
         x <- p$data$x
     }
 
     if (is.null(breaks)) {
         breaks <- hist(x, breaks=5, plot=FALSE)$breaks
     }
     m <- attr(p, "mapping")
 
     if (!is.null(mrsd) &&class(m$to) == "Date") {
         to <- Date2decimal(m$to)
     } else {
         to <- m$to
     }

     idx <- which(sapply(breaks, function(x) any(x > m$to)))
     if (length(idx)) {
         breaks <- breaks[-idx]
     }

     if (is.null(labels)) {
         labels <- breaks
     }

     breaks <- c(breaks, to)
     labels <- c(labels, gsub("\\.", "", as.character(m$from)))
 
     if (!is.null(mrsd) && class(p$data$x) == "Date") {
         p <- p + scale_x_date(breaks=decimal2Date(breaks), labels)
     } else {
         p <- p + scale_x_continuous(breaks=breaks, labels=labels)
     }

     return(p)

 }
 
 
 
 ## ##' view tree and associated matrix
 ## ##'
 ## ##' @title gplot
 ## ##' @param p tree view
 ## ##' @param data matrix
 ## ##' @param low low color
 ## ##' @param high high color
 ## ##' @param widths widths of sub plot
 ## ##' @param color color
 ## ##' @param font.size font size
 ## ##' @return list of figure
 ## ##' @importFrom gridExtra grid.arrange
 ## ##' @importFrom ggplot2 scale_x_continuous
 ## ##' @importFrom ggplot2 scale_y_continuous
 ## ##' @export
 ## ##' @author Guangchuang Yu \url{http://ygc.name}
 ## ##' @examples
 ## ##' nwk <- system.file("extdata", "sample.nwk", package="ggtree")
 ## ##' tree <- read.tree(nwk)
 ## ##' p <- ggtree(tree)
 ## ##' d <- matrix(abs(rnorm(52)), ncol=4)
 ## ##' rownames(d) <- tree$tip.label
 ## ##' colnames(d) <- paste0("G", 1:4)
 ## ##' gplot(p, d, low="green", high="red")
 ## gplot <- function(p, data, low="green", high="red", widths=c(0.5, 0.5), color="white", font.size=14) {
 ##     ## p <- p + scale_x_continuous(expand = c(0, 0)) + scale_y_continuous(expand = c(0, 0.6))
 ##     p1 <- p + scale_y_continuous(expand = c(0, 0.6))
 ##     ## p1 <- p + theme(panel.margin=unit(0, "null"))
 ##     ## p1 <- p1 + theme(plot.margin = unit(c(1, -1, 1.5, 1), "lines"))
 ##     p2 <- gplot.heatmap(p, data, low, high, color, font.size)
 ##     grid.arrange(p1, p2, ncol=2, widths=widths)
 ##     invisible(list(p1=p1, p2=p2))
 ## }
 
 
 ## ##' @importFrom grid unit
 ## ##' @importFrom ggplot2 scale_fill_gradient
 ## ##' @importFrom ggplot2 scale_fill_discrete
 ## ##' @importFrom ggplot2 element_text
 ## ##' @importFrom ggplot2 geom_tile
 ## ##' @importFrom ggplot2 labs
 ## ##' @importFrom ggplot2 guides
 ## ##' @importFrom ggplot2 guide_legend
 ## ##' @importFrom reshape2 melt
 ## gplot.heatmap <- function(p, data, low, high, color="white", font.size) {
 ##     isTip <- x <- Var1 <- Var2 <- value <- NULL
 ##     dd=melt(as.matrix(data))
 ##     ## p <- ggtree(tree) ## + theme_tree2()
 ##     ## p <- p + geom_text(aes(x = max(x)*1.1, label=label), subset=.(isTip), hjust=0)
 ##     ## p <- p+geom_segment(aes(x=x*1.02, xend=max(x)*1.08, yend=y), subset=.(isTip), linetype="dashed", size=0.4)
 ##     df=p$data
 ##     df=df[df$isTip,]

 ##     dd$Var1 <- factor(dd$Var1, levels = df$label[order(df$y)])
 ##     if (any(dd$value == "")) {
 ##         dd$value[dd$value == ""] <- NA
 ##     }

 ##     p2 <- ggplot(dd, aes(Var2, Var1, fill=value))+geom_tile(color=color)
 ##     if (is(dd$value,"numeric")) {
 ##         p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value="white")
 ##     } else {
 ##         p2 <- p2 + scale_fill_discrete(na.value="white")
 ##     }

 ##     p2 <- p2+xlab("")+ylab("")
 ##     p2 <- p2+theme_tree2() + theme(axis.ticks.x = element_blank(),
 ##                                    axis.line.x=element_blank())
 ##     ## p1 <- p1 + theme(axis.text.x = element_text(size = font.size))

 ##     p2 <- p2 + theme(axis.ticks.margin = unit(0, "lines"))

 ##     p2 <- p2 + theme(axis.text.x = element_text(size = font.size))
 ##     ## p2 <- p2 + theme(axis.text.y = element_text(size=font.size))

 
 ##     ## plot.margin   margin around entire plot (unit with the sizes of the top, right, bottom, and left margins)

 ##     ## units can be given in "lines" or  something more specific like "cm"...
 

 ##     p2 <- p2 + theme(panel.margin=unit(0, "null"))
 ##     p2 <- p2 + theme(plot.margin = unit(c(1, 1, .5, -0.5), "lines"))
 ##     p2 <- p2 + theme(legend.position = "right")
 ##     p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))
 ##     ## p2 <- p2 + labs(fill="")

 ##     return(p2)
 ## }
 
 
 coplot <- function(tree1, tree2, hjust=0) {
     x <- y <- label <- isTip <- tree <- NULL
     dx <- fortify(tree1)
     dx$tree <- "A"
 
     offset <- max(dx$x) * 1.3
     dy <- fortify(tree2)
     dy <- reverse.treeview.data(dy)
     dy$x <- dy$x + offset + hjust
     dy$tree <- "B"
 
     dd <- rbind(dx, dy)
     p <- ggplot(dd, aes(x, y)) +
         geom_tree(layout="phylogram", subset=.(tree=="A")) +
             geom_tree(layout="phylogram", subset=.(tree=="B")) +
                 theme_tree()

     p <- p  + geom_text(aes(label=label),
                         subset=.(isTip & tree == "A"),
                         hjust=-offset/40) +
                             geom_text(aes(label=label),
                                       subset=.(isTip & tree == "B"),
                                       hjust = offset/20)
     return(p)
 }