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| author | DannyArends | 2015-10-07 14:59:27 +0200 |
|---|---|---|
| committer | DannyArends | 2015-10-07 14:59:27 +0200 |
| commit | ce847df45dacefd2727ee05c58b54863251f2d5b (patch) | |
| tree | 99b4dc90ecc8843f1dec89e754fda1a976531f3f /wqflask | |
| parent | 4fb33d2ead790421957faeec0a6874f826a7cb9d (diff) | |
| download | genenetwork2-ce847df45dacefd2727ee05c58b54863251f2d5b.tar.gz | |
Passing more information calculated by WGCNA to the results page
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/wgcna/wgcna_analysis.py | 5 |
1 files changed, 4 insertions, 1 deletions
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index 9ab7950b..0cf4eeaf 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -74,6 +74,7 @@ class WGCNA(object): # Transfer the load data from python to R uStrainsR = r_unique(ro.Vector(strains)) # Unique strains in R vector uTraitsR = r_unique(ro.Vector(traits)) # Unique traits in R vector + self.phenotypes = uTraitsR r_cat("The number of unique strains:", r_length(uStrainsR), "\n") r_cat("The number of unique traits:", r_length(uTraitsR), "\n") @@ -93,7 +94,7 @@ class WGCNA(object): self.results = {} # Calculate a good soft threshold powers = r_c(r_c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10), r_seq(12, 20, 2)) - sft = self.r_pickSoftThreshold(rM, powerVector = powers, verbose = 5) + self.sft = self.r_pickSoftThreshold(rM, powerVector = powers, verbose = 5) # Create block wise modules using WGCNA network = self.r_blockwiseModules(rM, power = 6, verbose = 3) @@ -125,6 +126,8 @@ class WGCNA(object): print("Processing WGCNA output") template_vars = {} template_vars["input"] = self.input + template_vars["phenotypes"] = self.phenotypes + template_vars["powers"] = self.sft[1:] # Results from the soft threshold analysis template_vars["results"] = self.results self.render_image(results) sys.stdout.flush() |