mat_dist: Visualize distribution of a matrix or a list

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Visualize distribution of a matrix or a list

Usage

mat_dist(x, subgroup = NULL, reorder_column = TRUE, od = if(is.matrix(x)) seq_len(ncol(x)) else seq_along(x),
    ha = if(is.null(subgroup)) NULL else HeatmapAnnotation(subgroup = subgroup, show_annotation_name = TRUE),
    type = c("densityHeatmap", "MDS"), title = title, ...)

Arguments

x	a matrix or a list. If it is a matrix, distribution in columns are visualized
subgroup	subgroup information
reorder_column	if it is true, samples are first ordered by subgroups and in each subgroup, samples are ordered by median values
od	order of columns. If reorder_column is set to TRUE, this argument is ignored.
ha	Annotations that are specified as a HeatmapAnnotation-class object. The annotations will be put on top of the heatmap.
type	three types of plots are supported, see details
title	title for the plot
...	pass to densityHeatmap

Details

Three types of plots for visualizing distributions are supported:

densityHeatmap:

density of distribution is visualized as heatmaps, use densityHeatmap

lineplot:

distribution is visualized as normal line plot, use matplot

MDS:

multiple dimension scaling by calling cmdscale

Value

Order of columns in the heatmap

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
NULL

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.