EnrichedHeatmap (version 1.2.2)

anno_enriched: Annotation function to show the enrichment

Description

Annotation function to show the enrichment

Usage

anno_enriched(gp = gpar(col = "red"), pos_line = TRUE, pos_line_gp = gpar(lty = 2),
    yaxis = TRUE, ylim = NULL, value = c("mean", "sum"), yaxis_side = "right",
    yaxis_gp = gpar(fontsize = 8), show_error = FALSE)

Arguments

gp

graphic parameters

pos_line

whether draw vertical lines which represent the position of target

pos_line_gp

graphic parameters

yaxis

whether show yaxis

ylim

ranges on y-axis

value

what type of value corresponds to the y-axis

yaxis_side

side of y-axis

yaxis_gp

graphic parameters for yaxis

show_error

whether show error regions which are +-1 sd to the mean value. Color of error area is same as the corresponding lines with 75 percent transparency.

Value

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

Details

This annotation functions shows mean values of columns in the normalized matrix which represents the enrichment of the signals to the targets.

If rows are splitted, there will also be multiple lines in this annotation.

It should only be placed as column annotation of the Enriched Heatmap.

Examples

load(paste0(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, trim = c(0, 0.01))
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3",
    top_annotation = HeatmapAnnotation(lines = anno_enriched(gp = gpar(col = 2:4))), 
    top_annotation_height = unit(2, "cm"),
    km = 3, row_title_rot = 0)