EnrichedHeatmap: Constructor Method for the Enriched Heatmap

In jokergoo/EnrichedHeatmap: Making Enriched Heatmaps

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 <[e-mail]>

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

jokergoo/EnrichedHeatmap documentation built on Feb. 27, 2024, 6:43 p.m.