load.R

flog.debug("Starting App", name="server")

getFileLocation <- function(entity) {
  entity$path
}

#source the heatmap code
source("expression_heatmap.R")

#source generic heatmap functions
source("generic_annotation_functions.R")

#get the global functions
source("global_functions.R")

###############################
## Load precomputed data
###############################

source("loadPrecomputedData.R")

###############################
## Load synapse data
###############################


## This may break!
## Cache the data thats actually used
# save(list=c("combined_metadata", "eset.mRNA", "eset.miRNA", "eset.meth", "meth_to_gene", "miRNA_to_genes", "pathways_list"),
#      file="cached_data.RData")
# f <- File("cached_data.RData", parentId="syn4108202")
# o <- synStore(f)

# Use only these metadata columns
metadataColsToUse <- c("Cell_Line_Type", "Reprogramming_Gene_Combination", 
                       "Reprogramming_Vector_Type", "Tissue_of_Origin", "Diffname_short",
                       "Cell_Type_of_Origin", "Gender", "Originating_Lab_ID",
                       "Cell_Line_of_Origin", "Donor_ID", "Originating_Lab", "Cell_Type",
                       "Culture_Conditions")
# metadataColsToUse <- c("Cell_Line_Type")
metadataIdCol <- "UID"

# cacheId <- "syn4108151"
cacheId <- NA
# cacheId <- "local"

if (!is.na(cacheId)) {
  ## Caching for testing
  if (cacheId == "local") {
    load("cached_data.RData")
  }
  else {
    o <- synGet(cacheId)
    load(getFileLocation(o))
  }
  flog.debug("Using cached data loaded from Synapse", name="server")
} else {
  #get the MSigDB data
  source("msigdb_data_prep.R")
  
  #get the mRNA expression data
  source("mRNA_data_prep.R")
  
  #get the miRNA expression data
  source("miRNA_data_prep.R")
  
  #get the methylation data
  source("methylation_data_prep.R")
  
  #prepare single global metadata
  combined_metadata <- rbind(mRNA_metadata, miRNA_metadata, meth_metadata, deparse.level = 0)
  
  # Sample column required for expression matrix filtering
  combined_metadata$Sample <- rownames(combined_metadata)
}