EnrichedHeatmap: Constructor Method for the Enriched Heatmap
In EnrichedHeatmap: Making Enriched Heatmaps

Description Usage Arguments Details Value Author(s) Examples

Constructor Method for the Enriched Heatmap

EnrichedHeatmap(mat,
    col,
    top_annotation = HeatmapAnnotation(enriched = anno_enriched()),
    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 `normalizeToMatrix`.
`col`	Color settings. If the signals are categorical, color should be a vector with category levels as names.
`top_annotation`	A special annotation which is always put on top of the enriched heatmap and is constructed by `anno_enriched`.
`row_order`	Row order. Default rows are ordered by enriched scores calculated from `enriched_score`.
`pos_line`	Whether draw vertical lines which represent the positions of `target`?
`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` is a vector of length three which corresponds to upstream, target itself and downstream. If the targets are regions with width larger than 1, `axis_name` should be a vector of length four which corresponds to upstream, start of targets, end of targets and downstream.
`axis_name_rot`	Rotation for axis names.
`axis_name_gp`	Graphic parameters for axis names.
`border`	Whether show the border of the heatmap?
`cluster_rows`	Clustering on rows are turned off by default.
`show_row_dend`	Whether show dendrograms on rows if hierarchical clustering is applied 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. `at` and `labels` can not be set here.
`...`	Other arguments passed to `Heatmap`.

The enriched heatmap is essentially a normal heatmap but with several special settings. 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

EnrichedHeatmap calls Heatmap, thus, most of the arguments in Heatmap are usable in EnrichedHeatmap such as to apply clustering on rows, or to split rows by a data frame or k-means clustering. Users can also add more than one heatmaps by + operator. Enriched heatmaps and normal heatmaps can be concatenated mixed.

For detailed demonstration, please go to the vignette.

A Heatmap-class object.

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

Loading required package: grid
Loading required package: ComplexHeatmap
========================================
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))
========================================

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
========================================
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))
========================================

The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.
The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.
The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.