anno_enriched: Annotation function to show the enrichment

Description Usage Arguments Details Value Author(s) Examples

Description

Annotation function to show the enrichment

Usage

1
2
3
4
anno_enriched(gp = gpar(col = "red"), pos_line = TRUE, pos_line_gp = gpar(lty = 2),
    yaxis = TRUE, ylim = NULL, value = c("mean", "sum", "abs_mean", "abs_sum"), yaxis_side = "right",
    yaxis_facing = ifelse(yaxis_side == "right", "right", "left"),
    yaxis_gp = gpar(fontsize = 8), show_error = FALSE)

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 to draw vertical lines which represent positions of target

pos_line_gp

graphic parameters for the position lines

yaxis

whether show yaxis

ylim

ranges on y-axis, by default it is inferred from the data

value

the method to summarize signals from columns of the noramlized matrix

yaxis_side

side of y-axis

yaxis_facing

facing of the axis ticks and labels. It can be set to avoid overlapping text when multiple heatmaps are plotted together

yaxis_gp

graphic parameters for y-axis

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.

Details

This annotation functions shows mean values (or depends on the method set in value argument) of columns in the normalized matrix which represents 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 can be set to top_annotation argument in EnrichedHeatmap.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

1
2
3
4
5
6
7
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)

eilslabs/EnrichedHeatmap documentation built on May 16, 2019, 1:22 a.m.