diff options
| -rw-r--r-- | wqflask/wqflask/ctl/ctl_analysis.py | 26 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/ctl_setup.html | 46 |
2 files changed, 65 insertions, 7 deletions
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 44bade5c..77e34143 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -79,6 +79,18 @@ class CTL(object): self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')] self.trait_db_list = [x for x in self.trait_db_list if x] + print("strategy:", requestform.get("strategy")) + strategy = requestform.get("strategy") + + print("nperm:", requestform.get("nperm")) + nperm = int(requestform.get("nperm")) + + print("parametric:", requestform.get("parametric")) + parametric = bool(requestform.get("parametric")) + + print("significance:", requestform.get("significance")) + significance = float(requestform.get("significance")) + # Get the name of the .geno file belonging to the first phenotype datasetname = self.trait_db_list[0].split(":")[1] dataset = data_set.create_dataset(datasetname) @@ -120,26 +132,26 @@ class CTL(object): rPheno = r_data_frame(rPheno) rGeno = r_data_frame(rGeno) - r_write_table(rGeno, "~/outputGN/geno.csv") - r_write_table(rPheno, "~/outputGN/pheno.csv") + # Debug: Print the genotype and phenotype files to disk + #r_write_table(rGeno, "~/outputGN/geno.csv") + #r_write_table(rPheno, "~/outputGN/pheno.csv") # Perform the CTL scan - res = self.r_CTLscan(rGeno, rPheno, ncores = 6) + res = self.r_CTLscan(rGeno, rPheno, strategy = strategy, nperm = nperm, parametric = parametric, ncores = 6) # Get significant interactions - significant = self.r_CTLsignificant(res) - - print(significant[0]) + significant = self.r_CTLsignificant(res, significance = significance) # Create an image for output self.results = {} self.results['imgurl'] = webqtlUtil.genRandStr("WGCNAoutput_") + ".png" self.results['imgloc'] = GENERATED_IMAGE_DIR + self.results['imgurl'] self.results['ctlresult'] = significant + self.results['requestform'] = requestform # Store the user specified parameters for the output page # Create the lineplot r_png(self.results['imgloc'], width=1000, height=600) - self.r_lineplot(res) + self.r_lineplot(res, significance = significance) r_dev_off() # Flush any output from R diff --git a/wqflask/wqflask/templates/ctl_setup.html b/wqflask/wqflask/templates/ctl_setup.html index 0ba281c6..9c0d7bea 100644 --- a/wqflask/wqflask/templates/ctl_setup.html +++ b/wqflask/wqflask/templates/ctl_setup.html @@ -8,11 +8,57 @@ <form action="/ctl_results" method="post" class="form-horizontal"> <input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}"> + + <div class="dropdown"> + <label for="Strategy">Strategy</label> + <div class="col-sm-10"> + <select name="strategy" id="strategy"> + <option value="Exact">Exact</option> + <option value="Full">Full</option> + <option value="Pairwise">Pairwise</option> + </select> + </div> + </div> + + <div class="dropdown"> + <label for="Permutations">Number of permutation (Used when strategy is Full or Pairwise)</label> + <div class="col-sm-10"> + <select name="nperm" id="nperm"> + <option value="100">100</option> + <option value="1000" selected="selected">1000</option> + <option value="10000">10000</option> + </select> + </div> + </div> + + <div class="dropdown"> + <label for="Coefficient">Type of correlation coefficient</label> + <div class="col-sm-10"> + <select name="parametric" id="parametric"> + <option value="False">Spearman</option> + <option value="True">Pearson</option> + </select> + </div> + </div> + + + <div class="dropdown"> + <label for="Significance">Significance level</label> + <div class="col-sm-10"> + <select name="significance" id="significance"> + <option value="0.1">0.1</option> + <option value="0.05" selected="selected">0.05</option> + <option value="0.001">0.001</option> + </select> + </div> + </div> + <br> <div class="form-group"> <div class="col-sm-10"> <input type="submit" class="btn btn-primary" value="Run CTL using these settings" /> </div> </div> + </form> </div> |