boxplotViewer: Visualization of cluster enrichment profiles conditions

In tchitchek-lab/SPADEVizR: SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Visualization of cluster enrichment profiles conditions

Description

The Boxplot Viewer aims to visualize and compare the abundances between several biological conditions for one single cluster or for a set of combined clusters.

This representation displays cell cluster abundances of each biological condition using boxplots. Additionally, the abundance density of each biological condition can be visualize using violin representation. Cluster abundance of each sample can also be visualized via colored dots.

Abundance from several clusters can be a by providing one or several cluster names to the 'clusters' parameter. Biological conditions information must be assigned to the samples in order to use this viewer (provided by the slot 'assignments' in the 'Results' object). The cell cluster abundances could be displayed as percentages or absolute numbers using the 'use.percentages' parameter (TRUE by default).

Usage

boxplotViewer(Results, samples = NULL, clusters = NULL,
  use.percentages = TRUE, show.legend = TRUE, show.violin = TRUE,
  show.on_device = TRUE)

Arguments

Results	a 'Results' object
samples	a character vector providing the sample names to used (all samples by default)
clusters	a character vector containing the clusters names to be visualized (required)
use.percentages	a logical specifying if the visualization must be performed on percentage
show.legend	a logical specifying if the legend must be displayed
show.violin	a logical specifying if the count distribution must be displayed
show.on_device	a logical specifying if the representation will be displayed on device

Details

Biological conditions are specified in the Results object at the importation or using the 'assignContext()' function. Cells clusters are colored based on theirs associated biological samples.

Value

a 'ggplot' object

tchitchek-lab/SPADEVizR documentation built on Jan. 27, 2024, 8:58 p.m.