gplots: heatmap.2 – R documentation

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heatmap.2

Enhanced Heat Map

Description

A heat map is a false color image (basically image(t(x))) with a dendrogram added to the left side and/or to the top. Typically, reordering of the rows and columns according to some set of values (row or column means) within the restrictions imposed by the dendrogram is carried out.

This heatmap provides a number of extensions to the standard R heatmap function.

Usage

heatmap.2 (x,

           # dendrogram control
           Rowv = TRUE,
           Colv=if(symm)"Rowv" else TRUE,
           distfun = dist,
           hclustfun = hclust,
           dendrogram = c("both","row","column","none"),
           reorderfun = function(d, w) reorder(d, w),
           symm = FALSE,

           # data scaling
           scale = c("none","row", "column"),
           na.rm=TRUE,

           # image plot
           revC = identical(Colv, "Rowv"),
           add.expr,

           # mapping data to colors
           breaks,
           symbreaks=any(x < 0, na.rm=TRUE) || scale!="none",

           # colors
           col="heat.colors",

           # block sepration
           colsep,
           rowsep,
           sepcolor="white",
           sepwidth=c(0.05,0.05),

           # cell labeling
           cellnote,
           notecex=1.0,
           notecol="cyan",
           na.color=par("bg"),

           # level trace
           trace=c("column","row","both","none"),
           tracecol="cyan",
           hline=median(breaks),
           vline=median(breaks),
           linecol=tracecol,

           # Row/Column Labeling
           margins = c(5, 5),
           ColSideColors,
           RowSideColors,
           cexRow = 0.2 + 1/log10(nr),
           cexCol = 0.2 + 1/log10(nc),
           labRow = NULL,
           labCol = NULL,
           srtRow = NULL,
           srtCol = NULL,
           adjRow = c(0,NA),
           adjCol = c(NA,0),
           offsetRow = 0.5,
           offsetCol = 0.5,
           colRow = NULL,
           colCol = NULL,

           # color key + density info
           key = TRUE,
           keysize = 1.5,
           density.info=c("histogram","density","none"),
           denscol=tracecol,
           symkey = any(x < 0, na.rm=TRUE) || symbreaks,
           densadj = 0.25,
           key.title = NULL,
           key.xlab = NULL,
           key.ylab = NULL,
           key.xtickfun = NULL,
           key.ytickfun = NULL,
           key.par=list(),

           # plot labels
           main = NULL,
           xlab = NULL,
           ylab = NULL,

           # plot layout
           lmat = NULL,
           lhei = NULL,
           lwid = NULL,

           # extras
           extrafun=NULL,
           ...
           )

Arguments

`x`	numeric matrix of the values to be plotted.
`Rowv`	determines if and how the row dendrogram should be reordered. By default, it is TRUE, which implies dendrogram is computed and reordered based on row means. If NULL or FALSE, then no dendrogram is computed and no reordering is done. If a `dendrogram`, then it is used "as-is", ie without any reordering. If a vector of integers, then dendrogram is computed and reordered based on the order of the vector.
`Colv`	determines if and how the column dendrogram should be reordered. Has the options as the `Rowv` argument above and additionally when `x` is a square matrix, `Colv="Rowv"` means that columns should be treated identically to the rows.
`distfun`	function used to compute the distance (dissimilarity) between both rows and columns. Defaults to `dist`.
`hclustfun`	function used to compute the hierarchical clustering when `Rowv` or `Colv` are not dendrograms. Defaults to `hclust`.
`dendrogram`	character string indicating whether to draw 'none', 'row', 'column' or 'both' dendrograms. Defaults to 'both'. However, if Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a warning is issued and Rowv (or Colv) arguments are honoured.
`reorderfun`	`function(d, w)` of dendrogram and weights for reordering the row and column dendrograms. The default uses `stats{reorder.dendrogram}`

symm

logical indicating if x should be treated symmetrically; can only be true when x is a square matrix.

`scale`	character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. The default is `"none"`.
`na.rm`	logical indicating whether `NA`'s should be removed.

`revC`	logical indicating if the column order should be `rev`ersed for plotting, such that e.g., for the symmetric case, the symmetry axis is as usual.
`add.expr`	expression that will be evaluated after the call to `image`. Can be used to add components to the plot.
`breaks`	(optional) Either a numeric vector indicating the splitting points for binning `x` into colors, or a integer number of break points to be used, in which case the break points will be spaced equally between `min(x)` and `max(x)`.
`symbreaks`	Boolean indicating whether breaks should be made symmetric about 0. Defaults to `TRUE` if the data includes negative values, and to `FALSE` otherwise.
`col`	colors used for the image. Defaults to heat colors (`heat.colors`).

`colsep, rowsep, sepcolor`	(optional) vector of integers indicating which columns or rows should be separated from the preceding columns or rows by a narrow space of color `sepcolor`.
`sepwidth`	(optional) Vector of length 2 giving the width (colsep) or height (rowsep) the separator box drawn by colsep and rowsep as a function of the width (colsep) or height (rowsep) of a cell. Defaults to `c(0.05, 0.05)`

`cellnote`	(optional) matrix of character strings which will be placed within each color cell, e.g. p-value symbols.
`notecex`	(optional) numeric scaling factor for `cellnote` items.
`notecol`	(optional) character string specifying the color for `cellnote` text. Defaults to "cyan".
`na.color`	Color to use for missing value (`NA`). Defaults to the plot background color.

`trace`	character string indicating whether a solid "trace" line should be drawn across 'row's or down 'column's, 'both' or 'none'. The distance of the line from the center of each color-cell is proportional to the size of the measurement. Defaults to 'column'.
`tracecol`	character string giving the color for "trace" line. Defaults to "cyan".
`hline, vline, linecol`	Vector of values within cells where a horizontal or vertical dotted line should be drawn. The color of the line is controlled by `linecol`. Horizontal lines are only plotted if `trace` is 'row' or 'both'. Vertical lines are only drawn if `trace` 'column' or 'both'. `hline` and `vline` default to the median of the breaks, `linecol` defaults to the value of `tracecol`.

`margins`	numeric vector of length 2 containing the margins (see `par(mar= *)`) for column and row names, respectively.
`ColSideColors`	(optional) character vector of length `ncol(x)` containing the color names for a horizontal side bar that may be used to annotate the columns of `x`.
`RowSideColors`	(optional) character vector of length `nrow(x)` containing the color names for a vertical side bar that may be used to annotate the rows of `x`.
`cexRow, cexCol`	positive numbers, used as `cex.axis` in for the row or column axis labeling. The defaults currently only use number of rows or columns, respectively.
`labRow, labCol`	character vectors with row and column labels to use; these default to `rownames(x)` or `colnames(x)`, respectively.
`srtRow, srtCol`	angle of row/column labels, in degrees from horizontal
`adjRow, adjCol`	2-element vector giving the (left-right, top-bottom) justification of row/column labels (relative to the text orientation).
`offsetRow, offsetCol`	Number of character-width spaces to place between row/column labels and the edge of the plotting region.
`colRow, colCol`	color of row/column labels, either a scalar to set the color of all labels the same, or a vector providing the colors of each label item

`key`	logical indicating whether a color-key should be shown.
`keysize`	numeric value indicating the size of the key
`density.info`	character string indicating whether to superimpose a 'histogram', a 'density' plot, or no plot ('none') on the color-key.
`denscol`	character string giving the color for the density display specified by `density.info`, defaults to the same value as `tracecol`.
`symkey`	Boolean indicating whether the color key should be made symmetric about 0. Defaults to `TRUE` if the data includes negative values, and to `FALSE` otherwise.
`densadj`	Numeric scaling value for tuning the kernel width when a density plot is drawn on the color key. (See the `adjust` parameter for the `density` function for details.) Defaults to 0.25.
`key.title`	main title of the color key. If set to NA no title will be plotted.
`key.xlab`	x axis label of the color key. If set to NA no label will be plotted.
`key.ylab`	y axis label of the color key. If set to NA no label will be plotted.
`key.xtickfun`	function computing tick location and labels for the xaxis of the color key. Returns a named list containing parameters that can be passed to `axis`. See examples.
`key.ytickfun`	function computing tick location and labels for the y axis of the color key. Returns a named list containing parameters that can be passed to `axis`. See examples.
`key.par`	graphical parameters for the color key. Named list that can be passed to `par`.

main, xlab, ylab

main, x- and y-axis titles; defaults to none.

`lmat, lhei, lwid`	visual layout: position matrix, column height, column width. See below for details
`extrafun`	A function to be called after all other work. See examples.
`...`	additional arguments passed on to `image`

Details

If either Rowv or Colv are dendrograms they are honored (and not reordered). Otherwise, dendrograms are computed as dd <- as.dendrogram(hclustfun(distfun(X))) where X is either x or t(x).

If either is a vector (of “weights”) then the appropriate dendrogram is reordered according to the supplied values subject to the constraints imposed by the dendrogram, by reorder(dd, Rowv), in the row case. If either is missing, as by default, then the ordering of the corresponding dendrogram is by the mean value of the rows/columns, i.e., in the case of rows, Rowv <- rowMeans(x, na.rm=na.rm). If either is NULL, no reordering will be done for the corresponding side.

If scale="row" (or scale="col") the rows (columns) are scaled to have mean zero and standard deviation one. There is some empirical evidence from genomic plotting that this is useful.

The default colors range from red to white (heat.colors) and are not pretty. Consider using enhancements such as the RColorBrewer package, https://cran.r-project.org/package=RColorBrewer to select better colors.

By default four components will be displayed in the plot. At the top left is the color key, top right is the column dendrogram, bottom left is the row dendrogram, bottom right is the image plot. When RowSideColor or ColSideColor are provided, an additional row or column is inserted in the appropriate location. This layout can be overriden by specifiying appropriate values for lmat, lwid, and lhei. lmat controls the relative postition of each element, while lwid controls the column width, and lhei controls the row height. See the help page for layout for details on how to use these arguments.

Value

Invisibly, a list with components

`rowInd`	row index permutation vector as returned by `order.dendrogram`.
`colInd`	column index permutation vector.
`call`	the matched call
`rowMeans, rowSDs`	mean and standard deviation of each row: only present if `scale="row"`
`colMeans, colSDs`	mean and standard deviation of each column: only present if `scale="column"`
`carpet`	reordered and scaled 'x' values used generate the main 'carpet'
`rowDendrogram`	row dendrogram, if present
`colDendrogram`	column dendrogram, if present
`breaks`	values used for color break points
`col`	colors used
`vline`	center-line value used for column trace, present only if `trace="both"` or `trace="column"`
`hline`	center-line value used for row trace, present only if `trace="both"` or `trace="row"`
`colorTable`	A three-column data frame providing the lower and upper bound and color for each bin
`layout`	A named list containing the values used for `lmat`, `lhei`, and `lwid`.

Note

The original rows and columns are reordered to match the dendrograms Rowv and Colv (if present).

heatmap.2() uses layout to arragent the plot elements. Consequentially, it can not be used in a multi column/row layout using layout(...), par(mfrow=...) or (mfcol=...).

Author(s)

Andy Liaw, original; R. Gentleman, M. Maechler, W. Huber, G. Warnes, revisions.

Examples

data(mtcars)
 x  <- as.matrix(mtcars)
 rc <- rainbow(nrow(x), start=0, end=.3)
 cc <- rainbow(ncol(x), start=0, end=.3)

 ##
 ## demonstrate the effect of row and column dendrogram options
 ##
 heatmap.2(x)                    ## default - dendrogram plotted and reordering done.
 heatmap.2(x, dendrogram="none") ##  no dendrogram plotted, but reordering done.
 heatmap.2(x, dendrogram="row")  ## row dendrogram plotted and row reordering done.
 heatmap.2(x, dendrogram="col")  ## col dendrogram plotted and col reordering done.

 heatmap.2(x, keysize=2)         ## default - dendrogram plotted and reordering done.

 heatmap.2(x, Rowv=FALSE, dendrogram="both") ## generates a warning!
 heatmap.2(x, Rowv=NULL, dendrogram="both")  ## generates a warning!
 heatmap.2(x, Colv=FALSE, dendrogram="both") ## generates a warning!

 ## Reorder dendrogram by branch means rather than sums
 heatmap.2(x, reorderfun=function(d, w) reorder(d, w, agglo.FUN = mean) )

 ## plot a sub-cluster using the same color coding as for the full heatmap
 full <- heatmap.2(x)
 heatmap.2(x, Colv=full$colDendrogram[[2]], breaks=full$breaks)  # column subset
 heatmap.2(x, Rowv=full$rowDendrogram[[1]], breaks=full$breaks)  # row subset
 heatmap.2(x, Colv=full$colDendrogram[[2]],
              Rowv=full$rowDendrogram[[1]], breaks=full$breaks)  # both

 ## Show effect of row and column label rotation
 heatmap.2(x, srtCol=NULL)
 heatmap.2(x, srtCol=0,   adjCol = c(0.5,1) )
 heatmap.2(x, srtCol=45,  adjCol = c(1,1)   )
 heatmap.2(x, srtCol=135, adjCol = c(1,0)   )
 heatmap.2(x, srtCol=180, adjCol = c(0.5,0) )
 heatmap.2(x, srtCol=225, adjCol = c(0,0)   ) ## not very useful
 heatmap.2(x, srtCol=270, adjCol = c(0,0.5) )
 heatmap.2(x, srtCol=315, adjCol = c(0,1)   )
 heatmap.2(x, srtCol=360, adjCol = c(0.5,1) )

 heatmap.2(x, srtRow=45, adjRow=c(0, 1) )
 heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=45, adjCol=c(1,1) )
 heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=270, adjCol=c(0,0.5) )


 ## Show effect of offsetRow/offsetCol (only works when srtRow/srtCol is
 ## not also present)
 heatmap.2(x, offsetRow=0, offsetCol=0)
 heatmap.2(x, offsetRow=1, offsetCol=1)
 heatmap.2(x, offsetRow=2, offsetCol=2)
 heatmap.2(x, offsetRow=-1, offsetCol=-1)

 heatmap.2(x, srtRow=0, srtCol=90, offsetRow=0, offsetCol=0)
 heatmap.2(x, srtRow=0, srtCol=90, offsetRow=1, offsetCol=1)
 heatmap.2(x, srtRow=0, srtCol=90, offsetRow=2, offsetCol=2)
 heatmap.2(x, srtRow=0, srtCol=90, offsetRow=-1, offsetCol=-1)


 ## Show how to use 'extrafun' to replace the 'key' with a scatterplot
 lmat <- rbind( c(5,3,4), c(2,1,4) )
 lhei <- c(1.5, 4)
 lwid <- c(1.5, 4, 0.75)

 myplot <- function() {
             oldpar <- par("mar")
             par(mar=c(5.1, 4.1, 0.5, 0.5))
             plot(mpg ~ hp, data=x)
           }

 heatmap.2(x, lmat=lmat, lhei=lhei, lwid=lwid, key=FALSE, extrafun=myplot)

 ## show how to customize the color key
 heatmap.2(x,
           key.title=NA, # no title
           key.xlab=NA,  # no xlab
           key.par=list(mgp=c(1.5, 0.5, 0),
                        mar=c(2.5, 2.5, 1, 0)),
           key.xtickfun=function() {
                 breaks <- parent.frame()$breaks
                 return(list(
                      at=parent.frame()$scale01(c(breaks[1],
                                                  breaks[length(breaks)])),
                      labels=c(as.character(breaks[1]),
                               as.character(breaks[length(breaks)]))
                      ))
           })

 heatmap.2(x,
          breaks=256,
          key.title=NA,
          key.xlab=NA,
          key.par=list(mgp=c(1.5, 0.5, 0),
                       mar=c(1, 2.5, 1, 0)),
          key.xtickfun=function() {
               cex <- par("cex")*par("cex.axis")
               side <- 1
               line <- 0
               col <- par("col.axis")
               font <- par("font.axis")
               mtext("low", side=side, at=0, adj=0,
                     line=line, cex=cex, col=col, font=font)
               mtext("high", side=side, at=1, adj=1,
                     line=line, cex=cex, col=col, font=font)
               return(list(labels=FALSE, tick=FALSE))
          })


 ##
 ## Show effect of z-score scaling within columns, blue-red color scale
 ##
 hv <- heatmap.2(x, col=bluered, scale="column", tracecol="#303030")

 ###
 ## Look at the return values
 ###
 names(hv)

 ## Show the mapping of z-score values to color bins
 hv$colorTable

 ## Extract the range associated with white
 hv$colorTable[hv$colorTable[,"color"]=="#FFFFFF",]

 ## Determine the original data values that map to white
 whiteBin <- unlist(hv$colorTable[hv$colorTable[,"color"]=="#FFFFFF",1:2])
 rbind(whiteBin[1] * hv$colSDs + hv$colMeans,
       whiteBin[2] * hv$colSDs + hv$colMeans )
 ##
 ## A more decorative heatmap, with z-score scaling along columns
 ##
 hv <- heatmap.2(x, col=cm.colors(255), scale="column",
	       RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
	       xlab="specification variables", ylab= "Car Models",
	       main="heatmap(<Mtcars data>, ..., scale=\"column\")",
         tracecol="green", density="density")
 ## Note that the breakpoints are now symmetric about 0

 ## Color the labels to match RowSideColors and ColSideColors
 hv <- heatmap.2(x, col=cm.colors(255), scale="column",
         RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
	       xlab="specification variables", ylab= "Car Models",
	       main="heatmap(<Mtcars data>, ..., scale=\"column\")",
         tracecol="green", density="density", colRow=rc, colCol=cc,
         srtCol=45, adjCol=c(0.5,1))





 data(attitude)
 round(Ca <- cor(attitude), 2)
 symnum(Ca) # simple graphic

 # with reorder
 heatmap.2(Ca, 		 symm=TRUE, margin=c(6, 6), trace="none" )

 # without reorder
 heatmap.2(Ca, Rowv=FALSE, symm=TRUE, margin=c(6, 6), trace="none" )

 ## Place the color key below the image plot
 heatmap.2(x, lmat=rbind( c(0, 3), c(2,1), c(0,4) ), lhei=c(1.5, 4, 2 ) )

 ## Place the color key to the top right of the image plot
 heatmap.2(x, lmat=rbind( c(0, 3, 4), c(2,1,0 ) ), lwid=c(1.5, 4, 2 ) )

 ## For variable clustering, rather use distance based on cor():
 data(USJudgeRatings)
 symnum( cU <- cor(USJudgeRatings) )

 hU <- heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=topo.colors(16),
              distfun=function(c) as.dist(1 - c), trace="none")

 ## The Correlation matrix with same reordering:
 hM <- format(round(cU, 2))
 hM

 # now with the correlation matrix on the plot itself

 heatmap.2(cU, Rowv=FALSE, symm=TRUE, col=rev(heat.colors(16)),
             distfun=function(c) as.dist(1 - c), trace="none",
             cellnote=hM)

 ## genechip data examples
 ## Not run: 
 library(affy)
 data(SpikeIn)
 pms <- SpikeIn@pm

 # just the data, scaled across rows
 heatmap.2(pms, col=rev(heat.colors(16)), main="SpikeIn@pm",
              xlab="Relative Concentration", ylab="Probeset",
              scale="row")

 # fold change vs "12.50" sample
 data <- pms / pms[, "12.50"]
 data <- ifelse(data>1, data, -1/data)
 heatmap.2(data, breaks=16, col=redgreen, tracecol="blue",
               main="SpikeIn@pm Fold Changes\nrelative to 12.50 sample",
               xlab="Relative Concentration", ylab="Probeset")
 
## End(Not run)

gplots

Various R Programming Tools for Plotting Data

v3.1.1

GPL-2

Authors

Gregory R. Warnes [aut], Ben Bolker [aut], Lodewijk Bonebakker [aut], Robert Gentleman [aut], Wolfgang Huber [aut], Andy Liaw [aut], Thomas Lumley [aut], Martin Maechler [aut], Arni Magnusson [aut], Steffen Moeller [aut], Marc Schwartz [aut], Bill Venables [aut], Tal Galili [ctb, cre]

Initial release

2020-11-28