correlatedClustersViewer: Visualization of correlated clusters

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

Visualization of correlated clusters

Description

Generates a volcano plot representation showing for each cluster: its correlation coefficient and associated p-value.

This representation displays the p-value (shown as -log10(p-value)) in the Y-axis and the correlation coefficient in the X-axis, in a two-dimensional chart. Each dot in the representation corresponds to a cell cluster, and both correlation coefficient (positive and negative) and p-value thresholds are shown using red dashed lines. Correlated Clusters are highlighted in red and labeled. The size of dots is proportional to the total number of associated cells in the considered samples.

Usage

correlatedClustersViewer(CC, show.cluster_sizes = TRUE,
  show.all_labels = FALSE, show.on_device = TRUE,
  max.dots_size = max([e-mail]), varname = NULL)

Arguments

CC	an object of class 'CC' (object returned by the 'computeCC()' function)
show.cluster_sizes	a logical specifying if dot sizes are proportional to number of associated cells
show.all_labels	a logical specifying if all cluster labels must be shown. Only labels of significant clusters are displayed otherwise
show.on_device	a logical specifying if the ggplot representation must be displayed on the device
max.dots_size	a numeric specifying the number of associated cells in the largest dot
varname	a character indicating the name of the variable to display in the title

Details

By default, only significant correlated clusters are labeled. Labels for all clusters can be displayed by setting the 'all.label' parameter to TRUE.

Value

a 'ggplot' object

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