biplotViewer: Visualization of marker co-expression

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

Visualization of marker co-expression

Description

The Biplot Viewer aims to visualize co-expressions between 2 markers using a biplot representation. In such representation, each cell is represented by a dot which is positioned in a two-dimensional space corresponding to the marker expressions.

Usage

biplotViewer(Results, x.marker, y.marker, samples = NULL,
  clusters = NULL, resample.ratio = NULL, sample.merge = FALSE,
  show.on_device = TRUE, use.percentage = FALSE)

Arguments

Results	a 'Results' object (with 'flowset' slot not null)
x.marker	a character indicating the marker name of the first dimension
y.marker	a character indicating the marker name of the second dimension
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 used)
resample.ratio	a numeric ratio (between 0 and 1) specifying the down-sampling ratio to show less dots (or NULL)
sample.merge	a logical specifying if the selected samples must be merged in a single biplot
show.on_device	a logical specifying if the representation will be displayed on device
use.percentage	a logical specifying if the number of cells must be provided as percentages of parents

Details

Cells coming from specific clusters or samples can be selected using the 'clusters' and 'samples' parameters. Moreover, samples can be displayed independently (default behaviour) or merged. In order to seed-up the computations, the number of cells to display can be down-sampled using the 'resample.ratio' parameter.

Value

a 'ggplot' object

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