volcanoViewer: Visualization of differentially abundant clusters

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

Visualization of differentially abundant clusters

Description

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

This representation displays the p-value (shown as -log10(p-value)) in the Y-axis and the fold-change of cell abundances, in the X-axis in a two-dimensional chart. Each dot in the representation corresponds to a cell cluster, and both p-value and fold-change thresholds are shown using red dashed lines. Differentially Abundant Clusters are highlighted in red and labeled. The size of dots is proportional to the total number of associated cells in the 2 conditions merged.

Usage

volcanoViewer(DAC = NULL, fc.log2 = TRUE, show.cluster_sizes = TRUE,
  show.all_labels = FALSE, show.on_device = TRUE,
  max.dots_size = max([e-mail]), y.max = NULL)

Arguments

DAC	an object of class 'DAC' (object returned by the 'computeDAC()' function)
fc.log2	a logical specifying if the fold-change or the log2(fold-change) must be used
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
y.max	a numeric specifying the maximal value of the y axis

Details

By default, only significant differentially abundant 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.