selectSpots: selectSpots

In Spaniel: Spatial Transcriptomics Analysis

Description

A function to select spots to remove from analysis

Usage

selectSpots(sObj, imgObj)

Arguments

sObj	Either a Seurat object (version 3) or a SingleCellExperiment object containing barcode coordinates in the metadata (Seurat) or colData (SingleCellExperiment).
imgObj	a ggplot grob (see parseImage function)

Value

Runs a shiny application

Examples

## Run the shiny app (Not run):
# selectSpots(sObj, imgObj)

# Click on the spots to remove from downstream analysis. Once all the spots 
# have been selected close the shiny app window. A list of spots is 
# stored in a text file called points_to_remove.txt in the working directory.

# Once this step has been run a filtered Seurat or SCE object can be 
# created using removeSpots (see removeSpots for more details)

Spaniel documentation built on Nov. 8, 2020, 5:54 p.m.