Some more work on the analysis

1 files changed, 26 insertions, 13 deletions

diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index 45c87d3f..5b6c1c1b 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -20,23 +20,36 @@ r_c             = ro.r["c"]                   # Map the c function
 r_seq           = ro.r["seq"]                 # Map the seq function
 r_table         = ro.r["table"]               # Map the table function
 r_names         = ro.r["names"]               # Map the names function
+r_sink          = ro.r["sink"]                # Map the sink function
+r_file          = ro.r["file"]                # Map the file function
 r_png           = ro.r["png"]                 # Map the png function for plotting
 r_dev_off       = ro.r["dev.off"]             # Map the dev.off function
 
-
-#TODO: This should only be done once, since it is quite expensive
-print(r_library("WGCNA"))                     # Load WGCNA
-print(r_options(stringsAsFactors = False))
-
-
-
 class WGCNA(object):
-    def __init__(self, start_vars):
+    def __init__(self):
         print("Initialization of WGCNA")
-
-    def run_wgcna(self):
-        print("Starting WGCNA analysis")
-
-    def process_wgcna_results(self, results):
+        log = r_file("/tmp/genenetwork_wcgna.log", open = "wt")
+        #r_sink(log)                                  # Uncomment the r_sink() commands to log output from stdout/stderr to a file
+        #r_sink(log, type = "message")
+        r_library("WGCNA")                            # Load WGCNA - Should only be done once, since it is quite expensive
+        r_options(stringsAsFactors = False)
+        print("Initialization of WGCNA done, package loaded in R session")
+        r_enableWGCNAThreads    = ro.r["enableWGCNAThreads"]        # Map the enableWGCNAThreads function
+        r_pickSoftThreshold     = ro.r["pickSoftThreshold"]         # Map the pickSoftThreshold function
+        r_blockwiseModules      = ro.r["blockwiseModules"]          # Map the blockwiseModules function
+        r_labels2colors         = ro.r["labels2colors"]             # Map the labels2colors function
+        r_plotDendroAndColors   = ro.r["plotDendroAndColors"]       # Map the plotDendroAndColors function
+        print("Obtained pointers to WGCNA functions")
+
+    def run_analysis(self, requestform):
+        print("Starting WGCNA analysis on dataset")
+        results = {}
+
+    def process_results(self, results):
         print("Processing WGCNA output")
+        template_vars = {}
+        template_vars["result"] = "OK"
+        #r_sink(type = "message")                                   # This restores R output to the stdout/stderr
+        #r_sink()                                                   # We should end the Rpy session more or less
+        return(dict(template_vars))