diff options
| -rw-r--r-- | wqflask/wqflask/wgcna/wgcna_analysis.py | 24 |
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 |