EnrichedHeatmap {EnrichedHeatmap} | R Documentation

## Constructor method for EnrichedHeatmap class

### Description

Constructor method for EnrichedHeatmap class

### Usage

    EnrichedHeatmap(mat, col, top_annotation = HeatmapAnnotation(enriched = anno_enriched()),
        top_annotation_height = unit(2, "cm"),
        row_order = order(enriched_score(mat), decreasing = TRUE), pos_line = TRUE,
        pos_line_gp = gpar(lty = 2), axis_name = NULL, axis_name_rot = 0,
        axis_name_gp = gpar(fontsize = 10), border = TRUE, cluster_rows = FALSE,
        row_dend_reorder = -enriched_score(mat),
        show_row_dend = FALSE, show_row_names = FALSE,
        heatmap_legend_param = list(), ...)

### Arguments

`mat` | a matrix which is returned by `normalizeToMatrix`
`col` | color settings. If the signals are categorical, color should be a vector with category levels as names.
`top_annotation` | a specific annotation which is always put on top of the enriched heatmap and is constructed by `anno_enriched`
`top_annotation_height` | the height of the top annotation
`row_order` | row order. Default rows are ordered by enriched scores calculated from `enriched_score`
`pos_line` | whether draw vertical lines which represent the positions of `target`
`pos_line_gp` | graphic parameters for the position lines
`axis_name` | names for axis which is below the heatmap. If the targets are single points, `axis_name` is a vector of length three which corresponds to upstream, target itself and downstream. If the targets are regions with width larger than 1, `axis_name` should be a vector of length four which corresponds to upstream, start of targets, end of targets and downstream.
`axis_name_rot` | rotation for axis names
`axis_name_gp` | graphic parameters for axis names
`border` | whether show border of the heatmap
`cluster_rows` | clustering on rows are turned off by default
`show_row_dend` | whether show dendrograms on rows if apply hierarchical clustering on rows
`row_dend_reorder` | weight for reordering the row dendrogram. It is reordered by enriched scores by default.
`show_row_names` | whether show row names
`heatmap_legend_param` | a list of settings for heatmap legends. `at` and `labels` can not be set here.
`...` | pass to `Heatmap`

### Details

`EnrichedHeatmap-class` is inherited from `Heatmap-class`. Following parameters are set with pre-defined values:

`cluster_columns`

  enforced to be `FALSE`

`show_column_names`

  enforced to be `FALSE`

`bottom_annotation`

  enforced to be `NULL`

`column_title_side`

  enforced to be `top`

A `EnrichedHeatmap-class` object is also a `Heatmap-class` object, thus, most of the arguments in `Heatmap` are usable in `EnrichedHeatmap` such as to apply clustering on rows, or to split rows by data frame or k-means clustering. Users can also add more than one heatmaps by `+` operator. For a detailed demonstration, please go to the vignette.

### Value

An `EnrichedHeatmap-class` object which is inherited from `Heatmap-class`.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### Examples

    load(system.file("extdata", "chr21_test_data.RData", package = "EnrichedHeatmap"))
    mat3 = normalizeToMatrix(meth, cgi, value_column = "meth", mean_mode = "absolute",
        extend = 5000, w = 50, smooth = TRUE)
    EnrichedHeatmap(mat3, name = "methylation", column_title = "methylation near CGI")
    EnrichedHeatmap(mat3, name = "meth1") + EnrichedHeatmap(mat3, name = "meth2")
    # for more examples, please go to the vignette

[Package EnrichedHeatmap version 1.9.4 Index]