runShinySpaniel {Spaniel} | R Documentation |
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.
runShinySpaniel()
Runs a Shiny App
## 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()