R/ggheatmap.R

In hbc/CHBUtils: "Useful utility functions used at the core"

# copied wholesale from https://github.com/chr1swallace/random-functions
 
## colours, generated by
## library(RColorBrewer)
## rev(brewer.pal(11,name="RdYlBu"))

 
mydplot <- function(ddata, row=!col, col=!row, labels=col) {
  require(ggplot2)
  ## plot a dendrogram
  yrange <- range(ddata$segments$y)
  yd <- yrange[2] - yrange[1]
  nc <- max(nchar(as.character(ddata$labels$label)))
  tangle <- if(row) { 0 } else { 90 }
  tshow <- col
  p <- ggplot() +
        geom_segment(data=segment(ddata), aes(x=x, y=y, xend=xend, yend=yend)) +
        labs(x = NULL, y = NULL) + theme_dendro()
  if(row) {
    p <- p +
      scale_x_continuous(expand=c(0.5/length(ddata$labels$x),0)) +
      theme(axis.text.y = element_text(hjust=1)) +
        coord_flip()
  } else {
    p <- p +
      theme(axis.text.x = element_text(angle = 90, hjust = 1))
  }
return(p)
}
 
g_legend<-function(a.gplot){
## from
## http://stackoverflow.com/questions/11883844/inserting-a-table-under-the-legend-in-a-ggplot2-histogram
  tmp <- ggplot_gtable(ggplot_build(a.gplot))
  leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
  legend <- tmp$grobs[[leg]]
  return(legend)
}

##' Display a ggheatmap
##'
##' this function sets up some viewports, and tries to plot the dendrograms to line up with the heatmap
##' @param L a list with 3 named plots: col, row, centre, generated by ggheatmap
##' @param col.width,row.width number between 0 and 1, fraction of the device devoted to the column or row-wise dendrogram. If 0, don't print the dendrogram
##' @return no return value, side effect of displaying plot in current device
##' @export
##' @author Chris Wallace
ggheatmap.show <- function(L, col.width=0.2, row.width=0.2) {
  require(grid)
  require(ggplot2)
grid.newpage()
top.layout <- grid.layout(nrow = 2, ncol = 2,
widths = unit(c(1-row.width,row.width), "null"),
heights = unit(c(col.width,1-row.width), "null"))
pushViewport(viewport(layout=top.layout))
if(col.width>0)
print(L$col, vp=viewport(layout.pos.col=1, layout.pos.row=1))
if(row.width>0)
print(L$row, vp=viewport(layout.pos.col=2, layout.pos.row=2))
## print centre without legend
print(L$centre +
theme(axis.line=element_blank(),
axis.text.x=element_blank(),axis.text.y=element_blank(),
axis.ticks=element_blank(),
axis.title.x=element_blank(),axis.title.y=element_blank(),
legend.position="none",
panel.background=element_blank(),
panel.border=element_blank(),panel.grid.major=element_blank(),
panel.grid.minor=element_blank(),plot.background=element_blank()),
vp=viewport(layout.pos.col=1, layout.pos.row=2))
## add legend
legend <- g_legend(L$centre)
pushViewport(viewport(layout.pos.col=2, layout.pos.row=1))
grid.draw(legend)
upViewport(0)
}

##' generate a heatmap + dendrograms, ggplot2 style
##'
##' @param x data matrix
##' @param hm.colours vector of colours (optional)
##' @return invisibly returns a list of ggplot2 objects. Display them with ggheatmap.show()
##' @author Chris Wallace
##' @export
##' @examples
##' ## test run
##' ## simulate data
##' library(mvtnorm)
##' sigma=matrix(0,10,10)
##' sigma[1:4,1:4] <- 0.6
##' sigma[6:10,6:10] <- 0.8
##' diag(sigma) <- 1
##' X <- rmvnorm(n=100,mean=rep(0,10),sigma=sigma)
##'  
##' ## make plot
##' p <- ggheatmap(X)
##'  
##' ## display plot
##' ggheatmap.show(p)
ggheatmap <- function(x,
                      hm.colours= c("#ffffcc", "#ffeda0", "#fed976",
                        "#feb24c", "#fd8d3c", "#fc4e2a", "#e31a1c",
                        "#bd0026", "#800026")) {
  require(ggdendro)
  require(ggplot2)
  require(reshape)
  require(grid)
  #my.colours = rev(c("#ffffcc", "#ffeda0", "#fed976", "#feb24c", "#fd8d3c",
  #  "#fc4e2a", "#e31a1c", "#bd0026", "#800026"))
  if(is.null(colnames(x)))
    colnames(x) <- sprintf("col%s",1:ncol(x))
  if(is.null(rownames(x)))
    rownames(x) <- sprintf("row%s",1:nrow(x))
  ## plot a heatmap
  ## x is an expression matrix
  row.hc <- try(hclust(dist(x), "ward.D"),silent=T)
  if (class(row.hc)=="try-error"){
    row.hc <- try(hclust(dist(x), "ward"),silent=T)
  }
  col.hc <- try(hclust(dist(t(x)), "ward.D"),silent=T)
  if (class(col.hc)=="try-error"){
    col.hc <- try(hclust(dist(t(x)), "ward"),silent=T)
  }
  
  row.dendro <- dendro_data(as.dendrogram(row.hc),type="rectangle")
  col.dendro <- dendro_data(as.dendrogram(col.hc),type="rectangle")
 
  ## dendro plots
  col.plot <- mydplot(col.dendro, col=TRUE, labels=TRUE) +
        scale_x_continuous(breaks = 1:ncol(x),labels=col.hc$labels[col.hc$order]) +
        theme(plot.margin = unit(c(0,0,0,0), "lines"))
  row.plot <- mydplot(row.dendro, row=TRUE, labels=TRUE) +
        scale_x_continuous(breaks = 1:nrow(x),labels=row.hc$labels[row.hc$order]) +
        theme(plot.margin = unit(c(0,0,0,0), "lines"))
 
  ## order of the dendros
  col.ord <- match(col.dendro$labels$label, colnames(x))
  row.ord <- match(row.dendro$labels$label, rownames(x))
  xx <- x[row.ord,col.ord]
  dimnames(xx) <- NULL
  xx <- melt(xx)
 
  centre.plot <- ggplot(xx, aes(X2,X1)) + geom_tile(aes(fill=value), colour="white") +
        scale_fill_gradientn(colours = hm.colours) +
        labs(x = NULL, y = NULL) +
        scale_x_continuous(expand=c(0,0)) +
        scale_y_continuous(expand=c(0,0),breaks = NULL) +
        theme(plot.margin = unit(rep(0, 4), "lines"))
  ret <- list(col=col.plot,row=row.plot,centre=centre.plot)
  invisible(ret)
}