EnrichedHeatmap: Constructor method for EnrichedHeatmap class

Description

Constructor method for EnrichedHeatmap class

Usage

EnrichedHeatmap(mat, score_fun = enriched_score, row_order = NULL, pos_line = TRUE,
    pos_line_gp = gpar(lty = 2), axis_name = NULL, axis_name_rot = NULL,
    axis_name_gp = gpar(fontsize = 10), border = TRUE, cluster_rows = FALSE,
    show_row_dend = FALSE, ...)

Arguments

mat

a matrix which is returned by normalizeToMatrix

score_fun

a function which calculates enriched scores for rows in mat. This function can be self-defined, take a look at enriched_score to find out how to design it. Note if row clustering is turned on, this argument is ignored.

row_order

row order. If it is specified, score_fun is ignored.

pos_line

whether draw vertical lines which represent the position of target

pos_line_gp

graphic parameters for 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 border of the heatmap

cluster_rows

clustering on rows are turned off by default

show_row_dend

whether show dendrograms on rows

...

pass to Heatmap

Value

An EnrichedHeatmap-class object which is inherited from Heatmap-class.

Details

EnrichedHeatmap-class is inherited from Heatmap-class. Following parameters are set with pre-defined values:

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

With above pre-defined values, no graphics will be drawn below the heatmap, then the space below the heatmap can be used to add a new graph which contains the axis. A (or two) line which corresponds to the position of target will be added to the heatmap body as well.

Same as the Heatmap-class, users can make more controls on the heatmap such as apply clustering on rows, or split rows by data frame or k-means clustering. Users can also add more than one heatmaps by + operator.

For a detailed demonstration, please go to the vignette.

Examples

Run this code

load(paste0(system.file("extdata", "chr21_test_data.RData", 
    package = "EnrichedHeatmap")))
mat3 = normalizeToMatrix(meth, cgi, value_column = "meth", mean_mode = "absolute",
    extend = 5000, w = 50, empty_value = 0.5)
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