distogramViewer: Visualization of marker co-expressions

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

Visualization of marker co-expressions

Description

The Distogram Viewer aims to visualize the pairwise co-expressions between all markers using a distogram representation. In such representation, each tile corresponds to the co-expression between 2 markers and is gradient-colored based on the Pearson correlation between the expressions of those 2 markers (as stored in the phenotype matrix). Markers used as clustering markers are shown in blue.

Usage

distogramViewer(Results, samples = NULL, clusters = NULL,
  markers = NULL, 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 use (by default all clusters will be used)
markers	a character vector specifying the markers to be displayed
show.on_device	a logical specifying if the representation will be displayed on device

Details

The Pearson correlation is computed based on the marker expressions. The visualization can be restricted to specific clusters, samples and markers by using respectively the 'clusters', 'samples' and 'markers' parameters.

Value

a 'ggplot' object. This object also contains the correlations for each pair of marker (cor attribute).

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