diff options
| -rw-r--r-- | wqflask/wqflask/ctl/ctl_analysis.py | 56 |
1 files changed, 28 insertions, 28 deletions
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index e21b8500..3d2d7a37 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -79,6 +79,26 @@ class CTL(object): self.edges_list = [] print("Obtained pointers to CTL functions") + def addNode(self, gt): + node_dict = { 'data' : {'id' : str(gt.name) + ":" + str(gt.dataset.name), + 'sid' : str(gt.name), + 'dataset' : str(gt.dataset.name), + 'label' : gt.name, + 'symbol' : gt.symbol, + 'geneid' : gt.geneid, + 'omim' : gt.omim } } + self.nodes_list.append(node_dict) + + def addEdge(self, gtS, gtT, significant, x): + edge_data = {'id' : str(gtS.symbol) + '_' + significant[1][x] + '_' + str(gtT.symbol), + 'source' : str(gtS.name) + ":" + str(gtS.dataset.name), + 'target' : str(gtT.name) + ":" + str(gtT.dataset.name), + 'lod' : significant[3][x], + 'color' : "#ff0000", + 'width' : significant[3][x] } + edge_dict = { 'data' : edge_data } + self.edges_list.append(edge_dict) + def run_analysis(self, requestform): print("Starting CTL analysis on dataset") self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')] @@ -162,7 +182,7 @@ class CTL(object): self.r_lineplot(res, significance = significance) r_dev_off() - n = 2 + n = 2 # We start from 2, since R starts from 1 :) for trait in self.trait_db_list: # Create the QTL like CTL plots self.results['imgurl' + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png" @@ -175,23 +195,7 @@ class CTL(object): # Flush any output from R sys.stdout.flush() - # Create the interactive graph for cytoscape visualization (Nodes) - # TODO DA : make this a function - for trait in self.trait_db_list: - if trait != "": - ts = trait.split(':') - gt = TRAIT.GeneralTrait(name = ts[0], dataset_name = ts[1]) - node_dict = { 'data' : {'id' : str(gt.name) + ":" + str(gt.dataset.name), - 'sid' : str(gt.name), - 'dataset' : str(gt.dataset.name), - 'label' : gt.name, - 'symbol' : gt.symbol, - 'geneid' : gt.geneid, - 'omim' : gt.omim } } - self.nodes_list.append(node_dict) - - # Create the interactive graph for cytoscape visualization (Edges) - # TODO DA : make this a function + # Create the interactive graph for cytoscape visualization (Nodes and Edges) print(type(significant)) if not type(significant) == ri.RNULLType: for x in range(len(significant[0])): @@ -200,16 +204,12 @@ class CTL(object): tsT = significant[2][x].split(':') # Target gtS = TRAIT.GeneralTrait(name = tsS[0], dataset_name = tsS[1]) # Retrieve Source info from the DB gtT = TRAIT.GeneralTrait(name = tsT[0], dataset_name = tsT[1]) # Retrieve Target info from the DB - edge_data = {'id' : str(gtS.symbol) + '_' + significant[1][x] + '_' + str(gtT.symbol), - 'source' : str(gtS.name) + ":" + str(gtS.dataset.name), - 'target' : str(gtT.name) + ":" + str(gtT.dataset.name), - 'lod' : significant[3][x], - 'color' : "#ff0000", - 'width' : significant[3][x] } - edge_dict = { 'data' : edge_data } - self.edges_list.append(edge_dict) - significant[0][x] = gtS.symbol + " (" + gtS.name + ")" - significant[2][x] = gtT.symbol + " (" + gtT.name + ")" + self.addNode(gtS) + self.addNode(gtT) + self.addEdge(gtS, gtT, significant, x) + + significant[0][x] = gtS.symbol + " (" + gtS.name + ")" # Update the trait name for the displayed table + significant[2][x] = gtT.symbol + " (" + gtT.name + ")" # Update the trait name for the displayed table self.elements = json.dumps(self.nodes_list + self.edges_list) |