runShinySpaniel {Spaniel} | R Documentation

## RunShinySpaniel

### 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()

[Package Spaniel version 1.2.0 Index]