Constructor Method for the Enriched Heatmap

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

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)
#> All signal values are within [0, 1], so we assume it is methylation
#> signal. Automatically set limit [0, 1] to the smoothed values. If this
#> is not the case, set argument `limit = NA` in the function to remove
#> the limits. Set `verbose = FALSE` to turn off this message.
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