EnrichedHeatmap {EnrichedHeatmap} | R Documentation

## Constructor Method for the Enriched Heatmap

### Description

Constructor Method for the Enriched Heatmap

### Usage

    EnrichedHeatmap(mat,
        col,
        top_annotation = HeatmapAnnotation(enriched = anno_enriched()),
        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 special annotation which is always put on top of the enriched heatmap and is constructed by `anno_enriched`.
`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 the border of the heatmap?
`cluster_rows` | Clustering on rows are turned off by default.
`show_row_dend` | Whether show dendrograms on rows if hierarchical clustering is applied 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.
`...` | Other arguments passed to `Heatmap`.

### Details

The enriched heatmap is essentially a normal heatmap but with several special settings. 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`

`EnrichedHeatmap` calls `Heatmap`, thus, most of the arguments in `Heatmap` are usable in `EnrichedHeatmap` such as to apply clustering on rows, or to split rows by a data frame or k-means clustering. Users can also add more than one heatmaps by `+` operator. Enriched heatmaps and normal heatmaps can be concatenated mixed.

For detailed demonstration, please go to the vignette.

### Value

A `Heatmap-class` object.

### 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 1.17.1 Index]