# 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

1 |

### Arguments

`x` |
a matrix or a dissimilarity matrix of class dist. If a dissimilarity
matrix is used, then the |

`distfun` |
function used to compute the distance (dissimilarity) between
both rows and columns (default: |

`method` |
a character strings indicating the used seriation algorithm
(see |

`control` |
a list of control options passed on to the seriation
algorithm specified in |

`zlim` |
range of values to display (defaults to the range
of |

`...` |
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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
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))
``` |