abundantClustersViewer: Visualization of abundant clusters

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

Visualization of abundant clusters

Description

Generates a scatter plot representation showing for each cluster: its mean abundance and associated p-value.

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

Usage

abundantClustersViewer(AC, show.cluster_sizes = TRUE,
  show.all_labels = FALSE, show.on_device = TRUE,
  max.dots_size = max([e-mail]))

Arguments

AC	an object of class AC (object returned by the 'computeAC()' 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

Details

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

Value

a 'ggplot' object

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