From 5cfda8223a8ff56f27f6228fb1e35e94271bbdeb Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 9 Jan 2013 14:23:46 +0000
Subject: [PATCH] CCS-26 SP-446 : Show phenotype information from Chicago DB in
the strain browser
SVN: 28039
---
.../basynthec/browser/basynthec-browser.js | 105 +++++++++++++++---
1 file changed, 87 insertions(+), 18 deletions(-)
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-browser.js b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-browser.js
index f5817fc003c..a8273cef9a6 100644
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-browser.js
+++ b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-browser.js
@@ -451,6 +451,9 @@ function AppModel() {
// A map holding data sets by type
this.dataSetsByType = { };
+
+ // A set of all known growth media
+ this.growthMediaSet = {};
}
AppModel.prototype.initialize = function(callback) {
@@ -461,6 +464,15 @@ AppModel.prototype.initialize = function(callback) {
this.initializeOd600WithPhenotypesAndPredictionsModel(callback);
}
+AppModel.prototype.addGrowthMedium = function(medium, strain) {
+ var mediumList = this.growthMediaSet[medium];
+ if (null == mediumList) {
+ mediumList = [];
+ this.growthMediaSet[medium] = mediumList;
+ }
+ mediumList.push(strain);
+}
+
/** Compute the dataSetsByType variable */
AppModel.prototype.initializeDataSetsByType = function() {
// Group data sets by type
@@ -536,6 +548,13 @@ AppModel.prototype.initializeOd600WithPhenotypesAndPredictionsModel = function(c
for(strainName in model.dataSetsByStrain){
var strainData = strainDataMap[strainName];
var strainDatasets = model.dataSetsByStrain[strainName];
+ strainData.phenotypeMap = {};
+ if (strainData.hasPhenotypes) {
+ strainData.phenotypes.forEach(function(each) {
+ strainData.phenotypeMap[each.media] = each.relativeGrowth;
+ model.addGrowthMedium(each.media, strainName);
+ });
+ }
var hasPhenotypesOrPredictions = strainData && (strainData.hasPhenotypes || strainData.hasPredictions);
var hasOd600Datasets = strainDatasets && strainDatasets.dataSets.some(function(dataset){
@@ -580,6 +599,19 @@ AppModel.prototype.initializeOd600WithPhenotypesAndPredictionsModel = function(c
"mainGroupName" : "Strains without data in openBIS",
"groups" : createStrainGroups(strainsUnknownToOpenbisWithPhenotypesOrPredictions)
});
+
+ var commonGrowthMedia = []
+ var allGrowthMedia = []
+ for (medium in model.growthMediaSet) {
+ allGrowthMedia.push(medium);
+ if (model.growthMediaSet[medium].length > 20) {
+ commonGrowthMedia.push(medium);
+ }
+ }
+ allGrowthMedia.sort();
+ commonGrowthMedia.sort();
+ model.allGrowthMedia = allGrowthMedia;
+ model.commonGrowthMedia = commonGrowthMedia;
callback();
});
@@ -996,6 +1028,8 @@ Od600InspectorView.prototype.updateView = function(duration)
d.showSmall = !d.showSmall;
od600InspectorView.updateView();
});
+
+ appendGrowthSection(inspectorEnter);
appendObjectSection({
getSectionContainer: function(){
@@ -1014,24 +1048,6 @@ Od600InspectorView.prototype.updateView = function(duration)
return prediction_props_to_pairs(d);
}
});
-
- appendObjectSection({
- getSectionContainer: function(){
- return inspectorEnter;
- },
- getSectionName: function(){
- return "Phenotypes";
- },
- getSectionClass: function(){
- return "phenotypeSection";
- },
- getSectionObjects: function(d){
- return d.data.phenotypes ? d.data.phenotypes : [];
- },
- getSectionObjectProperties: function(d){
- return phenotype_props_to_pairs(d);
- }
- });
function graphWidth(d) { return d.showSmall ? GRAPH_SMALL_WIDTH : GRAPH_LARGE_WIDTH }
function graphHeight(d) { return d.showSmall ? GRAPH_SMALL_HEIGHT : GRAPH_LARGE_HEIGHT }
@@ -1156,6 +1172,59 @@ Od600InspectorView.prototype.updateView = function(duration)
.remove();
}
+function appendGrowthSection(inspectorEnter) {
+ var growthMediaSection = inspectorEnter.append("div");
+ var growsSection = growthMediaSection.selectAll("div.growth")
+ .data(function(d) { var growsOn = [];
+ model.allGrowthMedia.forEach(function(m) {
+ var value = d.data.phenotypeMap[m]
+ if (value && value > 0) growsOn.push(m);
+ });
+ return growsOn.length > 0 ? [growsOn] : [];
+ });
+ growsSection.enter().append("div")
+ .attr("class", "growth")
+ .text("Grows on: ");
+ growsSection.selectAll("span")
+ .data(function(d) { return d })
+ .enter().append("span")
+ .text(function (d) { return d + " "});
+
+ var doesNotGrowSection = growthMediaSection.selectAll("div.nogrow")
+ .data(function(d) { var doesNotGrowOn = [];
+ model.allGrowthMedia.forEach(function(m) {
+ var value = d.data.phenotypeMap[m]
+ if (value && value < 0.01) doesNotGrowOn.push(m);
+ });
+ return doesNotGrowOn.length > 0 ? [doesNotGrowOn] : [];
+ });
+ doesNotGrowSection.enter().append("div")
+ .attr("class", "nogrow")
+ .text("No growth on: ");
+ doesNotGrowSection.selectAll("span")
+ .data(function(d) { return d })
+ .enter().append("span")
+ .text(function (d) { return d + " "});
+
+
+ var unknownGrowthSection = growthMediaSection.selectAll("div.unknown")
+ .data(function(d) { var unknownGrowOn = [];
+ model.commonGrowthMedia.forEach(function(m) {
+ var value = d.data.phenotypeMap[m]
+ if (!value) unknownGrowOn.push(m);
+ });
+ return unknownGrowOn.length > 0 ? [unknownGrowOn] : [];
+ });
+ unknownGrowthSection.enter().append("div")
+ .attr("class", "unknown")
+ .text("Unknown growth on: ");
+
+ unknownGrowthSection.selectAll("span")
+ .data(function(d) { return d})
+ .enter().append("span")
+ .text(function (d) { return d + " "});
+}
+
function appendObjectSection(config){
var section = config.getSectionContainer().append("div")
--
GitLab