anno_enriched: Annotation Function to Show the Enrichment

In jokergoo/EnrichedHeatmap: Making Enriched Heatmaps

Annotation Function to Show the Enrichment

Description

Annotation Function to Show the Enrichment

Usage

anno_enriched(gp = gpar(col = "red"), pos_line = NULL, pos_line_gp = NULL,
    ylim = NULL, value = c("mean", "sum", "abs_mean", "abs_sum"),
    yaxis = TRUE, axis = yaxis, axis_param = list(side = "right"),
    show_error = FALSE, height = unit(2, "cm"), ...)

Arguments

gp	Graphic parameters. There are two non-standard parameters: neg_col and pos_col. If these two parameters are defined, the positive signals and negatie signals are visualized separatedly. The graphic parameters can be set as vectors when the heatmap or heatmap list is split into several row clusters.
pos_line	Whether draw vertical lines which represent positions of target?
pos_line_gp	Graphic parameters for the position lines.
ylim	Ranges on y-axis. By default it is inferred from the data.
value	The method to summarize signals from columns of the normalized matrix.
yaxis	Deprecated, use axis instead.
axis	Whether show axis?
axis_param	parameters for controlling axis. See default_axis_param for all possible settings and default parameters.
show_error	Whether show error regions which are one standard error to the mean value? Color of error area is same as the corresponding lines with 75 percent transparency.
height	Height of the annotation.
...	Other arguments.

Details

This annotation functions shows mean values (or depends on the method set in value argument) of columns in the normalized matrix which summarises the enrichment of the signals to the targets.

If rows are splitted, the enriched lines are calculated for each row cluster and there will also be multiple lines in this annotation viewport.

It should only be placed as column annotation of the enriched heatmap.

Value

A column annotation function which should be set to top_annotation argument in EnrichedHeatmap.

Author(s)

Zuguang Gu <[e-mail]>

Examples

load(system.file("extdata", "chr21_test_data.RData", package = "EnrichedHeatmap"))
tss = promoters(genes, upstream = 0, downstream = 1)
mat1 = normalizeToMatrix(H3K4me3, tss, value_column = "coverage", 
    extend = 5000, mean_mode = "w0", w = 50, keep = c(0, 0.99))
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3",
    top_annotation = HeatmapAnnotation(lines = anno_enriched(gp = gpar(col = 2:4))), 
    km = 3, row_title_rot = 0)

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