anno_enriched: Annotation Function to Show the Enrichment
In EnrichedHeatmap: Making Enriched Heatmaps

Description Usage Arguments Details Value Author(s) Examples

Annotation Function to Show the Enrichment

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"), ...)

`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.

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.

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

Zuguang Gu <z.gu@dkfz.de>

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)

Loading required package: grid
Loading required package: ComplexHeatmap
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ComplexHeatmap version 2.6.2
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
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Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
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EnrichedHeatmap version 1.20.0
Bioconductor page: http://bioconductor.org/packages/EnrichedHeatmap/
Github page: https://github.com/jokergoo/EnrichedHeatmap
Documentation: http://bioconductor.org/packages/EnrichedHeatmap/

If you use it in published research, please cite:
Gu, Z. EnrichedHeatmap: an R/Bioconductor package for comprehensive 
visualization of genomic signal associations. BMC Genomics 2018.

This message can be suppressed by:
  suppressPackageStartupMessages(library(EnrichedHeatmap))
========================================