deployshinycellapp.R

setwd()
#Install shiny cell
reqPkg = c("data.table", "Matrix", "hdf5r", "reticulate", "ggplot2", 
           "gridExtra", "glue", "readr", "RColorBrewer", "R.utils", "Seurat")
newPkg = reqPkg[!(reqPkg %in% installed.packages()[,"Package"])]
if(length(newPkg)){install.packages(newPkg)}

# If you are using h5ad file as input, run the code below as well
reticulate::py_install("anndata")

#To install shiny cell dependencies
reqPkg = c("shiny", "shinyhelper", "data.table", "Matrix", "DT", "hdf5r", 
           "reticulate", "ggplot2", "gridExtra", "magrittr", "ggdendro")
newPkg = reqPkg[!(reqPkg %in% installed.packages()[,"Package"])]
if(length(newPkg)){install.packages(newPkg)}

# To install shiny cell
devtools::install_github("SGDDNB/ShinyCell")


# To launch rds file
library(Seurat)
library(ShinyCell)

seu = readRDS("C:/Users/Cristal/Downloads/Baylor/shinycellexample/example.rds")
scConf = createConfig(seu)
makeShinyApp(seu, scConf, gene.mapping = TRUE,
             shiny.title = "DRG mouse atlas")