addProjection-Vision-method: Add a set of projection coordinates to use for visualization

In YosefLab/VISION: Functional interpretation of single cell RNA-seq latent manifolds

Add a set of projection coordinates to use for visualization

Description

By default VISION will run tSNE on the latent space and use this to display the cells in the output report. However, with this method, you may add additional two-dimensional coordinates for inclusion in the output report. This is useful if you have previously run tSNE (or any other visualization method) and wish to integrate the results into VISION.

Usage

## S4 method for signature 'Vision'
addProjection(object, name, coordinates)

Arguments

object	VISION object
name	Name of the projection
coordinates	numeric matrix or data.frame. Coordinates of each sample in the projection (NUM_SAMPLES x NUM_COMPONENTS)

Value

VISION object

Examples

## Not run: 

# First create the VISION object
vis <- Vision(data = expMat, signatures = sigs)

# Load and add an additional visualization
my_umap <- read.csv("umap_results.csv")
vis <- addProjection(vis, "UMAP", my_umap)

# Run analysis
vis <- analyze(vis)

# View results
viewResults(vis)


## End(Not run)

YosefLab/VISION documentation built on June 14, 2024, 5:27 p.m.