seriation: hmap – R documentation

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hmap

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

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))

seriation

Infrastructure for Ordering Objects Using Seriation

v1.2-9

GPL-3

Authors

Michael Hahsler [aut, cre, cph], Christian Buchta [aut, cph], Kurt Hornik [aut, cph], Fionn Murtagh [ctb, cph], Michael Brusco [ctb, cph], Stephanie Stahl [ctb, cph], Hans-Friedrich Koehn [ctb, cph]

Initial release

2020-09-29