# hmap

##### Plot Heat Map Reordered Using Seriation

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

- Keywords
- hplot

##### 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:

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

##### See Also

##### 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))
```

*Documentation reproduced from package seriation, version 1.2-2, License: GPL-3*