module_VST.R

# vst module
datasets <- 
  read_yaml("./data.yaml")
raw_data <- getwd()
t2g_hs <- read_rds("data/t2g_hs.rds")
t2g_mm <- read_rds("data/t2g_mm.rds")

vst_Server <- function(id, dataset_dds, dataset_choice) {
  moduleServer(id, function(input, output, session) {
    
    vst.create <- function(dds, dataset){
      
      dds.file <- dds
      
      vsd <- 
        vst(dds.file, blind = F)
      
      #mouse or human?
      is_hs <- grepl("t2g_hs", datasets[[dataset]]$t2g)
      
      if(is_hs){
        
        vst.table <- data.frame(assay(vsd)) %>% 
          rownames_to_column(., var = "ensembl_gene_id") %>% 
          left_join(unique(dplyr::select(t2g_hs, c(ensembl_gene_id, ext_gene))), ., by = 'ensembl_gene_id') %>%
          na.omit(.)
      } else {
        
        vst.table <- data.frame(assay(vsd)) %>% 
          rownames_to_column(., var = "ensembl_gene_id") %>% 
          left_join(unique(dplyr::select(t2g_mm, c(ensembl_gene_id, ext_gene))), ., by = 'ensembl_gene_id') %>%
          na.omit(.)
      }
      vst.table
    }
    vst.global <- reactive({
      vst.create(dataset_dds(), dataset_choice())
    })
    return(vst.global)
  })
}