countViewer: Visualization of cluster sizes

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

Visualization of cluster sizes

Description

The Count Viewer aims to visualize the number of cells associated to each cluster. This representation displays the clusters in the X-axis and the total number of associated cells in the Y-axis. Additionally, the numbers of cells associated to each cluster for each sample are also displayed using a jitter representation. The size of the dots is proportional to the total number of associated cells.

Usage

countViewer(Results, samples = NULL, clusters = NULL, min.cells = 0,
  sort = TRUE, max.dots_size = NULL, show.samples = 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 (by default all clusters will be displayed)
min.cells	a numeric specifying the minimum number of cell (sum of all selected samples) to display a cluster
sort	a logical specifying if the clusters will be to be sorted (descending) based on the sum of all selected samples for each cluster
max.dots_size	a numeric specifying the number of cells in the largest dot
show.samples	a logical specifying if the number of cells for all selected samples will be displayed
show.on_device	a logical specifying if the representation will be displayed on device

Details

By default, all clusters will be displayed but the representation can be restricted to a set of selected samples (using the 'samples' parameter) or to a set of selected clusters (using the 'clusters' parameter).

Value

a 'ggplot' object

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