EnrichedHeatmap {EnrichedHeatmap} | R Documentation |
Constructor method for EnrichedHeatmap class
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(), ...)
mat |
a matrix which is returned by |
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 |
top_annotation_height |
the height of the top annotation |
row_order |
row order. Default rows are ordered by enriched scores calculated from |
pos_line |
whether draw vertical lines which represent the positions of |
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_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. |
... |
pass to |
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.
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, 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