Description Usage Arguments Details Value Author(s) See Also Examples

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

1 |

`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. |

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`

.

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).

Michael Hahsler

`seriate`

,
`pimage`

,
`dissplot`

,
`heatmap.2`

in gplots.

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))
``` |

seriation documentation built on May 29, 2017, 9:18 a.m.

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