EnrichedHeatmap: Constructor method for EnrichedHeatmap class
In eilslabs/EnrichedHeatmap: Making Enriched Heatmaps

Description Usage Arguments Details Value Author(s) Examples

Constructor method for EnrichedHeatmap class

EnrichedHeatmap(mat, top_annotation = HeatmapAnnotation(enriched = anno_enriched()),
    top_annotation_height = unit(2, "cm"),
    score_fun = enriched_score, row_order = NULL, 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,
    show_row_dend = FALSE, show_row_names = FALSE, ...)

`mat`	a matrix which is returned by `normalizeToMatrix`
`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
`score_fun`	a function which calculates enriched scores for rows in `mat`. This function can be self-defined, refer to `enriched_score` to find out how to design it. Note if row clustering is turned on, this argument is ignored.
`row_order`	row order. If it is specified, `score_fun` is ignored.
`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
`show_row_names`	whether show row names
`...`	pass to `Heatmap`

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

row_order: the rows are sorted by the enriched score which is calculated by score_fun. The sorting is applied decreasingly.
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.

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

Zuguang Gu <z.gu@dkfz.de>

load(system.file("extdata", "chr21_test_data.RData", package = "EnrichedHeatmap"))
mat3 = normalizeToMatrix(meth, cgi, value_column = "meth", mean_mode = "absolute",
    extend = 5000, w = 50, background = 0.5)
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