Merge pull request #42 from Sage-Bionetworks/dev

merge develop
Sage-Bionetworks · Nov 29, 2017 · c2ce1cb · c2ce1cb
2 parents a02648d + beb2db3
commit c2ce1cb
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Showing 6 changed files with 447 additions and 412 deletions.
diff --git a/global.R b/global.R
@@ -24,78 +24,3 @@ flog.threshold(DEBUG, name='server')
 flog.threshold(DEBUG, name='ui')
 flog.threshold(DEBUG, name='global')
 flog.threshold(INFO, name='synapse')
-
-#login to synapse
-synapseLogin()
-
-flog.debug("Starting App", name="server")
-
-#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)
-}
diff --git a/load.R b/load.R
@@ -0,0 +1,71 @@
+flog.debug("Starting App", name="server")
+
+#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)
+}
diff --git a/msigdb_data_prep.R b/msigdb_data_prep.R
@@ -1,5 +1,5 @@
 #get the MsigDB object
 flog.info('Reading the MSIGDB object from synapse...', name='synapse')
-MSIGDB_syn<-synGet("syn2227979")
+MSIGDB_syn<-synGet("syn11519351")
 load(MSIGDB_syn@filePath) #available as MSigDB R object
 pathways_list <- c(MSigDB$C2.CP.BIOCARTA, MSigDB$C2.CP.KEGG, MSigDB$C2.CP.REACTOME)