runShinySpaniel: RunShinySpaniel

In Spaniel: Spatial Transcriptomics Analysis

Description

A function to visualise Spatial Transcriptomics. It requires a prepocessed Seurat Object or a SingleCellExperiment object as well as a rasterised image saved as an .rds object. There are 4 plots available in the app showing: a) the number of genes detected per spot, b) the number of reads detected per spot, c) clustering results, d) the gene expression of a selected gene." To view the clustering results the columns of the meta.data or colData containing clustering results must be prefixed with cluster_ . This can be done by using the markClusterCol() function included in Spaniel.

Usage

runShinySpaniel()

Value

Runs a Shiny App

Examples

## mark the columns of metadata/colData that contain clustering 
## information see ?markClusterCol for more details#'  
sObj <-  readRDS(file.path(system.file(package = "Spaniel"),
                    "extdata/SeuratData.rds"))
sObj <- markClusterCol(sObj, "res")

### parse background image
imgFile <- file.path(system.file(package = "Spaniel"),
            "HE_Rep1_resized.jpg")
img <- parseImage(imgFile)

## run shinySpaniel (upload data.rds and image.rds in the shiny app)
## Not Run:
# runShinySpaniel()

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