inst/spe_wrapper_app/app.R

In LieberInstitute/spatialLIBD: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

library("spatialLIBD")
library("markdown") ## due to a shinyapps.io bug

## spatialLIBD uses golem
options("golem.app.prod" = TRUE)

## You need this to enable shinyapps to install Bioconductor packages
options(repos = BiocManager::repositories())

## Load the data (all paths are relative to this script's location)
spe_wrapper <- readRDS("spe_wrapper.rds")
vars <- colnames(colData(spe_wrapper))

## Deploy the website
run_app(
    spe_wrapper,
    sce_layer = NULL,
    modeling_results = NULL,
    sig_genes = NULL,
    title = "spatialLIBD: human lymph node by 10x Genomics",
    spe_discrete_vars = c(vars[grep("10x_", vars)], "ManualAnnotation"),
    spe_continuous_vars = c("sum_umi", "sum_gene", "expr_chrM", "expr_chrM_ratio"),
    default_cluster = "10x_graphclust",
    docs_path = "www"
)