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-rw-r--r--wqflask/wqflask/wgcna/wgcna_analysis.py24
1 files changed, 11 insertions, 13 deletions
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index b5e01ece..1174ce47 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -87,17 +87,15 @@ class WGCNA(object):
for s in uStrainsR:
strain = s[0] # R uses vectors every single element is a vector
rM.rx[strain, trait] = self.input[trait].get(strain) # Update the matrix location
- #print(trait, strain, " in python: ", self.input[trait].get(strain), "in R:", rM.rx(strain,trait)[0])
+ #DEBUG: print(trait, strain, " in python: ", self.input[trait].get(strain), "in R:", rM.rx(strain,trait)[0])
sys.stdout.flush()
- # TODO: Get the user specified parameters
-
self.results = {}
- self.results['nphe'] = r_length(uTraitsR)[0]
- self.results['nstr'] = r_length(uStrainsR)[0]
- self.results['phenotypes'] = uTraitsR
- self.results['strains'] = uStrainsR
- self.results['requestform'] = requestform
+ self.results['nphe'] = r_length(uTraitsR)[0] # Number of phenotypes/traits
+ self.results['nstr'] = r_length(uStrainsR)[0] # Number of strains
+ self.results['phenotypes'] = uTraitsR # Traits used
+ self.results['strains'] = uStrainsR # Strains used in the analysis
+ self.results['requestform'] = requestform # Store the user specified parameters for the output page
# Calculate soft threshold if the user specified the SoftThreshold variable
if requestform.get('SoftThresholds') is not None:
@@ -109,14 +107,14 @@ class WGCNA(object):
print "PowerEstimate: {}".format(self.sft[0])
self.results['PowerEstimate'] = self.sft[0]
if r_is_NA(self.sft[0]):
- self.results['Power'] = 1
+ self.results['Power'] = 1 # No power could be estimated
else:
- self.results['Power'] = self.sft[0][0]
+ self.results['Power'] = self.sft[0][0] # Use the estimated power
else:
- # The user clicked a button, so no soft threshold selection, just use the value the user gives
- self.results['Power'] = requestform.get('Power')
+ # The user clicked a button, so no soft threshold selection
+ self.results['Power'] = requestform.get('Power') # Use the power value the user gives
- # Create block wise modules using WGCNA
+ # Create the block wise modules using WGCNA
network = self.r_blockwiseModules(rM, power = self.results['Power'], TOMType = requestform['TOMtype'], minModuleSize = requestform['MinModuleSize'], verbose = 3)
# Save the network for the GUI