R: Plot Heat Map Reordered Using Seriation

hmap {seriation} | R Documentation

## Plot Heat Map Reordered Using Seriation

### Description

Provides heat maps reordered using several different seriation methods. This includes dendrogram based reordering with optimal leaf order and matrix seriation based heat maps.

### Usage

    hmap(x, distfun = dist, method = "OLO", control = NULL, zlim = NULL, ...)

### Arguments

`x` | a matrix or a dissimilarity matrix of class dist. If a dissimilarity matrix is used, then the `distfun` is ignored.
`distfun` | function used to compute the distance (dissimilarity) between both rows and columns (default: `dist`).
`method` | a character strings indicating the used seriation algorithm (see `seriate.dist`). If the method results in a dendrogram then `heatmap` in stats is used to show the dendrograms, otherwise reordered distance matrices are shown instead.
`control` | a list of control options passed on to the seriation algorithm specified in `method`.
`zlim` | range of values to display (defaults to the range of `x`).
`...` | further arguments.

### Details

For dendrogram based heat maps the arguments are passed on to `heatmap.2` in gplots. See for example `margins` and `col`. The following arguments for `heatmap.2` cannot be used: `Rowv, Colv, hclustfun, reorderfun`.

For seriation-based heat maps further arguments include:

`gp`

  an object of class `gpar` containing graphical parameters (see `gpar` in package grid).

`newpage`

  a logical indicating whether to start plot on a new page (see `gpar` in package grid).

`prop`

  a logical indicating whether the height and width of `x` should be plotted proportional to its dimensions.

`showdist`

  Display seriated dissimilarity matrices? Values are `"none"`, `"both"`, `"rows"` or `"columns"`.

`key`

  logical; show a colorkey?.

key.lab

  string plotted next to the color key.

`axes`

  one of `"auto"` (default; show axis labels if there are less than 25 labels), `"x"`, `"y"`, `"both"` and `"none"`.

`margins`

  bottom and right-hand-side margins are calculated automatically or can be specifies as a vector of two numbers (in lines).

`zlim`

  range of values displayed.

`col`, `col_dist`

  color palettes used.

For `dendrogram = TRUE`, `seriate.hclust` with the default method `"optimal"` is used for arranging the dendrograms and `x`. `heatmap` is used for plotting.

For `dendrogram = FALSE`, `seriate.dist` with the default method `"tsp"` (a traveling salesperson solver) for arranging `x` is used. grid code implemented in this package is used to produce the plot.

Note that unlike the default behavior of `heatmap`, scaling is not automatically applied. The data have to be scaled before using `hmap`.

### Value

An invisible list with elements:

`rowInd, colInd` | index permutation vectors.
`reorder_method` | name of the method used to reorder the matrix.

The list may contain additional elements (dendrograms, colors, etc).

### Author(s)

Michael Hahsler

### See Also

`seriate`, `pimage`, `dissplot`, `heatmap.2` in gplots.

### Examples

    data("Wood")

    ## default heatmap does Euclidean distance, hierarchical clustering with
    ## average-link and optimal leaf ordering
    hmap(Wood)

    ## heatmap with correlation-based distance, green-red color (greenred is
    ## predefined) and optimal leaf ordering and no row label
    dist_cor <- function(x) as.dist(1-cor(t(x)))

    hmap(Wood, method="OLO", distfun = dist_cor, col=greenred(100), labRow=FALSE)

    ## order-based heatmap
    hmap(Wood, method="MDS_angle", distfun = dist_cor, col=greenred(100))

    ## order-based with dissimilarity matrices
    hmap(Wood, method="MDS_angle", distfun = dist_cor, showdist = "both",
      col=greenred(100))

[Package seriation version 1.2-8 Index]