diff options
| -rw-r--r-- | wqflask/wqflask/collect.py | 86 | ||||
| -rwxr-xr-x | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 35 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee | 85 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js | 60 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/marker_regression.coffee | 148 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/marker_regression.js | 88 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/collections/view.html | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression.html | 2 |
9 files changed, 392 insertions, 130 deletions
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 34def295..a77e19af 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -44,28 +44,54 @@ from wqflask import user_manager from base import trait +def get_collection(): + if g.user_session.logged_in: + return UserCollection() + else: + return AnonCollection() + #else: + # CauseError + class AnonCollection(object): """User is not logged in""" def __init__(self): self.anon_user = user_manager.AnonUser() - self.key = "anon_collection:v1:{}".format(self.anon_user.anon_id) - + self.key = "anon_collection:v4:{}".format(self.anon_user.anon_id) - def add_traits(params, collection_name): + def add_traits(self, params, collection_name): assert collection_name == "Default", "Unexpected collection name for anonymous user" + print("params[traits]:", params['traits']) traits = process_traits(params['traits']) - len_before = len(Redis.smembers) - Redis.sadd(self.key, traits) + print("traits is:", traits) + print("self.key is:", self.key) + len_before = len(Redis.smembers(self.key)) + Redis.sadd(self.key, *list(traits)) Redis.expire(self.key, 60 * 60 * 24 * 3) - len_now = len(Redis.smembers) + print("currently in redis:", Redis.smembers(self.key)) + len_now = len(Redis.smembers(self.key)) report_change(len_before, len_now) + def remove_traits(self, params): + traits_to_remove = params.getlist('traits[]') + print("traits_to_remove:", traits_to_remove) + len_before = len(Redis.smembers(self.key)) + Redis.srem(self.key, traits_to_remove) + len_now = len(Redis.smembers(self.key)) + print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now))) + + # We need to return something so we'll return this...maybe in the future + # we can use it to check the results + return str(len(members_now)) + def get_traits(self): + traits = Redis.smembers(self.key) + print("traits:", traits) + return traits class UserCollection(object): """User is logged in""" - def add_traits(params, collection_name): + def add_traits(self, params, collection_name): print("---> params are:", params.keys()) print(" type(params):", type(params)) if collection_name=="Default": @@ -94,15 +120,40 @@ class UserCollection(object): # Probably have to change that return redirect(url_for('view_collection', uc_id=uc.id)) + def remove_traits(self, params): + + #params = request.form + print("params are:", params) + uc_id = params['uc_id'] + uc = model.UserCollection.query.get(uc_id) + traits_to_remove = params.getlist('traits[]') + print("traits_to_remove are:", traits_to_remove) + traits_to_remove = process_traits(traits_to_remove) + print("\n\n after processing, traits_to_remove:", traits_to_remove) + all_traits = uc.members_as_set() + print(" all_traits:", all_traits) + members_now = all_traits - traits_to_remove + print(" members_now:", members_now) + print("Went from {} to {} members in set.".format(len(all_traits), len(members_now))) + uc.members = json.dumps(list(members_now)) + uc.changed_timestamp = datetime.datetime.utcnow() + db_session.commit() + + # We need to return something so we'll return this...maybe in the future + # we can use it to check the results + return str(len(members_now)) + def report_change(len_before, len_now): new_length = len_now - len_before if new_length: + print("We've added {} to your collection.".format( + numify(new_length, 'new trait', 'new traits'))) flash("We've added {} to your collection.".format( numify(new_length, 'new trait', 'new traits'))) else: - flash("No new traits were added.") + print("No new traits were added.") + - @app.route("/collections/add") @@ -128,7 +179,8 @@ def collections_new(): print("request.args in collections_new are:", params) if "anonymous_add" in params: - return add_anon_traits(params) + AnonCollection().add_traits(params, "Default") + return redirect(url_for('view_collection')) collection_name = params['new_collection'] @@ -143,8 +195,6 @@ def collections_new(): CauseAnError - - def process_traits(unprocessed_traits): print("unprocessed_traits are:", unprocessed_traits) if isinstance(unprocessed_traits, basestring): @@ -239,11 +289,9 @@ def view_collection(): uc_id = params['uc_id'] uc = model.UserCollection.query.get(uc_id) traits = json.loads(uc.members) + print("traits are:", traits) else: - anon_id = params['key'] - uc = model.AnonCollection(anon_id = anon_id) - traits = Redis.smembers(anon_id) - print("the traits are:", traits) + traits = AnonCollection().get_traits() print("in view_collection traits are:", traits) @@ -251,6 +299,7 @@ def view_collection(): json_version = [] for atrait in traits: + print("atrait is:", atrait) name, dataset_name = atrait.split(':') trait_ob = trait.GeneralTrait(name=name, dataset_name=dataset_name) @@ -267,8 +316,9 @@ def view_collection(): # dis=trait_ob.description)) #json_version.append(trait_ob.__dict__th) - collection_info = dict(trait_obs=trait_obs, - uc = uc) + #collection_info = dict(trait_obs=trait_obs, + # uc = uc) + collection_info = dict(trait_obs=trait_obs) if "json" in params: print("json_version:", json_version) return json.dumps(json_version) diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index a0ff31ef..04310083 100755 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -714,7 +714,9 @@ def main(): json_params = Redis.get(key) params = json.loads(json_params) - print("params:", params) + #print("params:", params) + + #print("kinship_matrix:", params['kinship_matrix']) tempdata = temp_data.TempData(params['temp_uuid']) if species == "human" : diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 7a3ae1e5..a46e33ee 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -1190,6 +1190,20 @@ class ShowTrait(object): print("-*- primary_samplelist is:", pf(primary_sample_names)) + other_sample_names = [] + for sample in this_trait.data.keys(): + if sample not in all_samples_ordered: + all_samples_ordered.append(sample) + other_sample_names.append(sample) + + other_sample_names, all_samples_ordered = get_samplelist_from_trait_data(this_trait, + all_samples_ordered) + + + print("species:", self.dataset.group.species) + if self.dataset.group.species == "human": + primary_sample_names += other_sample_names + primary_samples = SampleList(dataset = self.dataset, sample_names=primary_sample_names, this_trait=this_trait, @@ -1197,13 +1211,8 @@ class ShowTrait(object): header="%s Only" % (self.dataset.group.name)) print("primary_samples is: ", pf(primary_samples)) - other_sample_names = [] - for sample in this_trait.data.keys(): - if sample not in all_samples_ordered: - all_samples_ordered.append(sample) - other_sample_names.append(sample) - - if other_sample_names: + print("other_sample_names2:", other_sample_names) + if other_sample_names and self.dataset.group.species != "human": parent_f1_samples = None if self.dataset.group.parlist and self.dataset.group.f1list: parent_f1_samples = self.dataset.group.parlist + self.dataset.group.f1list @@ -1212,6 +1221,8 @@ class ShowTrait(object): if parent_f1_samples: other_sample_names = parent_f1_samples + other_sample_names + print("other_sample_names:", other_sample_names) + other_samples = SampleList(dataset=self.dataset, sample_names=other_sample_names, this_trait=this_trait, @@ -1227,3 +1238,13 @@ class ShowTrait(object): # or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))): # print("hjs") self.dataset.group.allsamples = all_samples_ordered + + +def get_samplelist_from_trait_data(this_trait, all_samples_ordered): + other_sample_names = [] + for sample in this_trait.data.keys(): + if sample not in all_samples_ordered: + all_samples_ordered.append(sample) + other_sample_names.append(sample) + + return other_sample_names, all_samples_ordered diff --git a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee index 30e6ea5e..74eb2e88 100644 --- a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee +++ b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.coffee @@ -29,6 +29,8 @@ class Chr_Manhattan_Plot @x_max = d3.max(@x_coords) @y_max = d3.max(@y_coords) * 1.2 + @y_threshold = @get_lod_threshold() + @svg = @create_svg() @plot_coordinates = _.zip(@x_coords, @y_coords, @marker_names) @@ -100,11 +102,20 @@ class Chr_Manhattan_Plot @y_scale = d3.scale.linear() .domain([@y_axis_filter, @y_max]) .range([@plot_height, @y_buffer]) + + get_lod_threshold: () -> + if @y_max/2 > 2 + return @y_max/2 + else + return 2 + create_graph: () -> @add_border() @add_x_axis() @add_y_axis() + @add_title() + @add_back_button() @add_plot_points() add_border: () -> @@ -164,7 +175,35 @@ class Chr_Manhattan_Plot .attr("class", "y_axis") .attr("transform", "translate(" + @x_buffer + ",0)") .call(@yAxis) - + + add_title: () -> + @svg.append("text") + .attr("class", "title") + .text("Chr " + @chr[0]) + .attr("x", (d) => + return (@plot_width + @x_buffer)/2 + ) + .attr("y", @y_buffer + 20) + .attr("dx", "0em") + .attr("text-anchor", "middle") + .attr("font-family", "sans-serif") + .attr("font-size", "18px") + .attr("fill", "black") + + add_back_button: () -> + @svg.append("text") + .attr("class", "back") + .text("Return to full view") + .attr("x", @x_buffer*2) + .attr("y", @y_buffer/2) + .attr("dx", "0em") + .attr("text-anchor", "middle") + .attr("font-family", "sans-serif") + .attr("font-size", "18px") + .attr("cursor", "pointer") + .attr("fill", "black") + .on("click", @return_to_full_view) + add_plot_points: () -> @plot_point = @svg.selectAll("circle") .data(@plot_coordinates) @@ -176,7 +215,20 @@ class Chr_Manhattan_Plot .attr("cy", (d) => return @y_scale(d[1]) ) - .attr("r", 2) + .attr("r", (d) => + if d[1] > 2 + return 3 + else + return 2 + ) + .attr("fill", (d) => + if d[1] > 2 + return "white" + else + return "black" + ) + .attr("stroke", "black") + .attr("stroke-width", "1") .attr("id", (d) => return "point_" + String(d[2]) ) @@ -187,16 +239,37 @@ class Chr_Manhattan_Plot this_id = "point_" + String(d[2]) d3.select("#" + this_id).classed("d3_highlight", true) .attr("r", 5) - .attr("fill", "yellow") + .attr("stroke", "none") + .attr("fill", "blue") .call(@show_marker_in_table(d)) ) .on("mouseout", (d) => this_id = "point_" + String(d[2]) d3.select("#" + this_id).classed("d3_highlight", false) - .attr("r", 2) - .attr("fill", "black") - #.call(@show_marker_in_table()) + .attr("r", (d) => + if d[1] > 2 + return 3 + else + return 2 + ) + .attr("fill", (d) => + if d[1] > 2 + return "white" + else + return "black" + ) + .attr("stroke", "black") + .attr("stroke-width", "1") ) + .append("svg:title") + .text((d) => + return d[2] + ) + + return_to_full_view: () -> + $('#manhattan_plot').remove() + $('#manhattan_plot_container').append('<div id="manhattan_plot"></div>') + root.manhattan_plot = new root.Manhattan_Plot show_marker_in_table: (marker_info) -> console.log("in show_marker_in_table") diff --git a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js index 2cbab00c..a38cfe5d 100644 --- a/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js +++ b/wqflask/wqflask/static/new/javascript/chr_manhattan_plot.js @@ -29,6 +29,7 @@ this.y_buffer = this.plot_height / 20; this.x_max = d3.max(this.x_coords); this.y_max = d3.max(this.y_coords) * 1.2; + this.y_threshold = this.get_lod_threshold(); this.svg = this.create_svg(); this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names); console.log("coordinates:", this.plot_coordinates); @@ -125,10 +126,20 @@ return this.y_scale = d3.scale.linear().domain([this.y_axis_filter, this.y_max]).range([this.plot_height, this.y_buffer]); }; + Chr_Manhattan_Plot.prototype.get_lod_threshold = function() { + if (this.y_max / 2 > 2) { + return this.y_max / 2; + } else { + return 2; + } + }; + Chr_Manhattan_Plot.prototype.create_graph = function() { this.add_border(); this.add_x_axis(); this.add_y_axis(); + this.add_title(); + this.add_back_button(); return this.add_plot_points(); }; @@ -164,27 +175,70 @@ return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(this.yAxis); }; + Chr_Manhattan_Plot.prototype.add_title = function() { + var _this = this; + return this.svg.append("text").attr("class", "title").text("Chr " + this.chr[0]).attr("x", function(d) { + return (_this.plot_width + _this.x_buffer) / 2; + }).attr("y", this.y_buffer + 20).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "black"); + }; + + Chr_Manhattan_Plot.prototype.add_back_button = function() { + return this.svg.append("text").attr("class", "back").text("Return to full view").attr("x", this.x_buffer * 2).attr("y", this.y_buffer / 2).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("cursor", "pointer").attr("fill", "black").on("click", this.return_to_full_view); + }; + Chr_Manhattan_Plot.prototype.add_plot_points = function() { var _this = this; return this.plot_point = this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", function(d) { return _this.x_scale(d[0]); }).attr("cy", function(d) { return _this.y_scale(d[1]); - }).attr("r", 2).attr("id", function(d) { + }).attr("r", function(d) { + if (d[1] > 2) { + return 3; + } else { + return 2; + } + }).attr("fill", function(d) { + if (d[1] > 2) { + return "white"; + } else { + return "black"; + } + }).attr("stroke", "black").attr("stroke-width", "1").attr("id", function(d) { return "point_" + String(d[2]); }).classed("circle", true).on("mouseover", function(d) { var this_id; console.log("d3.event is:", d3.event); console.log("d is:", d); this_id = "point_" + String(d[2]); - return d3.select("#" + this_id).classed("d3_highlight", true).attr("r", 5).attr("fill", "yellow").call(_this.show_marker_in_table(d)); + return d3.select("#" + this_id).classed("d3_highlight", true).attr("r", 5).attr("stroke", "none").attr("fill", "blue").call(_this.show_marker_in_table(d)); }).on("mouseout", function(d) { var this_id; this_id = "point_" + String(d[2]); - return d3.select("#" + this_id).classed("d3_highlight", false).attr("r", 2).attr("fill", "black"); + return d3.select("#" + this_id).classed("d3_highlight", false).attr("r", function(d) { + if (d[1] > 2) { + return 3; + } else { + return 2; + } + }).attr("fill", function(d) { + if (d[1] > 2) { + return "white"; + } else { + return "black"; + } + }).attr("stroke", "black").attr("stroke-width", "1"); + }).append("svg:title").text(function(d) { + return d[2]; }); }; + Chr_Manhattan_Plot.prototype.return_to_full_view = function() { + $('#manhattan_plot').remove(); + $('#manhattan_plot_container').append('<div id="manhattan_plot"></div>'); + return root.manhattan_plot = new root.Manhattan_Plot; + }; + Chr_Manhattan_Plot.prototype.show_marker_in_table = function(marker_info) { var marker_name; console.log("in show_marker_in_table"); diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee index 091dab93..44f4d9f7 100644 --- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee +++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee @@ -1,10 +1,11 @@ root = exports ? this class Manhattan_Plot - constructor: (@plot_height, @plot_width) -> + constructor: (@plot_height = 600, @plot_width = 1200) -> @qtl_results = js_data.qtl_results console.log("qtl_results are:", @qtl_results) @chromosomes = js_data.chromosomes + console.log("chromosomes are:", @chromosomes) @total_length = 0 @@ -31,6 +32,8 @@ class Manhattan_Plot console.log("@x_buffer: ", @x_buffer) @y_max = d3.max(@y_coords) * 1.2 + @y_threshold = @get_lod_threshold() + @svg = @create_svg() console.log("svg created") @@ -62,8 +65,6 @@ class Manhattan_Plot # ### - console.log("@chromosomes: ", @chromosomes) - cumulative_chr_lengths = [] chr_lengths = [] total_length = 0 @@ -97,16 +98,18 @@ class Manhattan_Plot chr_seen = [] for result in js_data.qtl_results if result.chr == "X" - chr_length = parseFloat(@chromosomes[20]) + chr_length = parseFloat(@chromosomes[13]) else - chr_length = parseFloat(@chromosomes[result.chr]) + chr_length = parseFloat(@chromosomes[result.chr]) + console.log("chr_seen is", chr_seen) if not(result.chr in chr_seen) chr_seen.push(result.chr) chr_lengths.push(chr_length) console.log("result.chr:", result.chr) console.log("total_length:", @total_length) if parseInt(result.chr) != 1 - console.log("plus:", chr_lengths.length - 2) + console.log("plus:", chr_lengths.length - 2) + console.log("chr_lengths.length", chr_lengths.length) @total_length += parseFloat(chr_lengths[chr_lengths.length - 2]) if result.lod_score > @y_axis_filter @x_coords.push(@total_length + parseFloat(result.Mb)) @@ -151,9 +154,10 @@ class Manhattan_Plot @add_y_axis() @add_axis_labels() @add_chr_lines() - #@fill_chr_areas() + @fill_chr_areas() @add_chr_labels() @add_plot_points() + #@create_zoom_pane() add_border: () -> @@ -298,51 +302,52 @@ class Manhattan_Plot ) .enter() .append("rect") - .attr("x", (d) => - if i == 0 - return @x_scale(0) - else - return @x_scale(d[1]) + .attr("x", (d, i) => + return @x_scale(d[1] - d[0]) ) - .attr("y", @y_buffer) - .attr("width", (d) => - return @x_scale(d[0]) + .attr("y", @y_buffer + 2) + .attr("width", (d, i) => + starting = @x_scale(d[1] - d[0]) + ending = @x_scale(@cumulative_chr_lengths[i]) + width = ending - starting + console.log("width:", d[0]) + return width ) - .attr("height", @plot_height-@y_buffer) - #.attr("fill", (d, i) => - # if i%2 - # return "whitesmoke" - # else - # return "none" - #) - - fill_chr_areas2: () -> - console.log("cumu_chr_lengths:", @cumulative_chr_lengths) - console.log("example:", @x_scale(@cumulative_chr_lengths[0])) - @svg.selectAll("rect.chr_fill_area") - .data(_.zip(@chr_lengths, @cumulative_chr_lengths), (d) => - return d - ) - .enter() - .append("rect") - .attr("x", (d) => - if i == 0 - return @x_scale(0) - else - return @x_scale(d[1]) - ) - .attr("y", @y_buffer) - .attr("width", (d) => - return @x_scale(d[0]) - ) - .attr("height", @plot_height-@y_buffer) + .attr("height", @plot_height-@y_buffer-3) .attr("fill", (d, i) => - return "whitesmoke" - #if i%2 - # return "whitesmoke" - #else - # return "none" + if (i+1)%2 + return "none" + else + return "whitesmoke" ) + + #fill_chr_areas2: () -> + # console.log("cumu_chr_lengths:", @cumulative_chr_lengths) + # console.log("example:", @x_scale(@cumulative_chr_lengths[0])) + # @svg.selectAll("rect.chr_fill_area") + # .data(_.zip(@chr_lengths, @cumulative_chr_lengths), (d) => + # return d + # ) + # .enter() + # .append("rect") + # .attr("x", (d) => + # if i == 0 + # return @x_scale(0) + # else + # return @x_scale(d[1]) + # ) + # .attr("y", @y_buffer) + # .attr("width", (d) => + # return @x_scale(d[0]) + # ) + # .attr("height", @plot_height-@y_buffer) + # .attr("fill", (d, i) => + # return "whitesmoke" + # #if i%2 + # # return "whitesmoke" + # #else + # # return "none" + # ) add_chr_labels: () -> chr_names = [] @@ -372,6 +377,7 @@ class Manhattan_Plot .attr("text-anchor", "middle") .attr("font-family", "sans-serif") .attr("font-size", "18px") + .attr("cursor", "pointer") .attr("fill", "black") .on("click", (d) => this_chr = d @@ -389,7 +395,20 @@ class Manhattan_Plot .attr("cy", (d) => return @y_scale(d[1]) ) - .attr("r", 2) + .attr("r", (d) => + if d[1] > 2 + return 3 + else + return 2 + ) + .attr("fill", (d) => + if d[1] > 2 + return "white" + else + return "black" + ) + .attr("stroke", "black") + .attr("stroke-width", "1") .attr("id", (d) => return "point_" + String(d[2]) ) @@ -400,15 +419,32 @@ class Manhattan_Plot this_id = "point_" + String(d[2]) d3.select("#" + this_id).classed("d3_highlight", true) .attr("r", 5) - .attr("fill", "yellow") + .attr("stroke", "none") + .attr("fill", "blue") .call(@show_marker_in_table(d)) ) .on("mouseout", (d) => this_id = "point_" + String(d[2]) d3.select("#" + this_id).classed("d3_highlight", false) - .attr("r", 2) - .attr("fill", "black") + .attr("r", (d) => + if d[1] > 2 + return 3 + else + return 2 + ) + .attr("fill", (d) => + if d[1] > 2 + return "white" + else + return "black" + ) + .attr("stroke", "black") + .attr("stroke-width", "1") ) + .append("svg:title") + .text((d) => + return d[2] + ) redraw_plot: (chr_ob) -> console.log("chr_name is:", chr_ob[0]) @@ -434,9 +470,7 @@ class Manhattan_Plot @svg.select("path.area").attr("d", area); @svg.select("path.line").attr("d", line); - - #console.time('Create manhattan plot') - #new Manhattan_Plot(600, 1200) - #console.timeEnd('Create manhattan plot') -root.Manhattan_Plot = new Manhattan_Plot(600, 1200) \ No newline at end of file +root.Manhattan_Plot = Manhattan_Plot + +new Manhattan_Plot(600, 1200) \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js index 86509316..1965e7aa 100644 --- a/wqflask/wqflask/static/new/javascript/marker_regression.js +++ b/wqflask/wqflask/static/new/javascript/marker_regression.js @@ -9,11 +9,12 @@ function Manhattan_Plot(plot_height, plot_width) { var _ref; - this.plot_height = plot_height; - this.plot_width = plot_width; + this.plot_height = plot_height != null ? plot_height : 600; + this.plot_width = plot_width != null ? plot_width : 1200; this.qtl_results = js_data.qtl_results; console.log("qtl_results are:", this.qtl_results); this.chromosomes = js_data.chromosomes; + console.log("chromosomes are:", this.chromosomes); this.total_length = 0; this.max_chr = this.get_max_chr(); this.x_coords = []; @@ -32,6 +33,7 @@ console.log("@x_max: ", this.x_max); console.log("@x_buffer: ", this.x_buffer); this.y_max = d3.max(this.y_coords) * 1.2; + this.y_threshold = this.get_lod_threshold(); this.svg = this.create_svg(); console.log("svg created"); this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names); @@ -68,7 +70,6 @@ */ var chr_lengths, cumulative_chr_lengths, key, this_length, total_length; - console.log("@chromosomes: ", this.chromosomes); cumulative_chr_lengths = []; chr_lengths = []; total_length = 0; @@ -110,10 +111,11 @@ for (_i = 0, _len = _ref.length; _i < _len; _i++) { result = _ref[_i]; if (result.chr === "X") { - chr_length = parseFloat(this.chromosomes[20]); + chr_length = parseFloat(this.chromosomes[13]); } else { chr_length = parseFloat(this.chromosomes[result.chr]); } + console.log("chr_seen is", chr_seen); if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) { chr_seen.push(result.chr); chr_lengths.push(chr_length); @@ -121,6 +123,7 @@ console.log("total_length:", this.total_length); if (parseInt(result.chr) !== 1) { console.log("plus:", chr_lengths.length - 2); + console.log("chr_lengths.length", chr_lengths.length); this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]); } } @@ -157,6 +160,7 @@ this.add_y_axis(); this.add_axis_labels(); this.add_chr_lines(); + this.fill_chr_areas(); this.add_chr_labels(); return this.add_plot_points(); }; @@ -266,33 +270,21 @@ console.log("example:", this.x_scale(this.cumulative_chr_lengths[0])); return this.svg.selectAll("rect.chr_fill_area").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), function(d) { return d; - }).enter().append("rect").attr("x", function(d) { - if (i === 0) { - return _this.x_scale(0); - } else { - return _this.x_scale(d[1]); - } - }).attr("y", this.y_buffer).attr("width", function(d) { - return _this.x_scale(d[0]); - }).attr("height", this.plot_height - this.y_buffer); - }; - - Manhattan_Plot.prototype.fill_chr_areas2 = function() { - var _this = this; - console.log("cumu_chr_lengths:", this.cumulative_chr_lengths); - console.log("example:", this.x_scale(this.cumulative_chr_lengths[0])); - return this.svg.selectAll("rect.chr_fill_area").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), function(d) { - return d; - }).enter().append("rect").attr("x", function(d) { - if (i === 0) { - return _this.x_scale(0); + }).enter().append("rect").attr("x", function(d, i) { + return _this.x_scale(d[1] - d[0]); + }).attr("y", this.y_buffer + 2).attr("width", function(d, i) { + var ending, starting, width; + starting = _this.x_scale(d[1] - d[0]); + ending = _this.x_scale(_this.cumulative_chr_lengths[i]); + width = ending - starting; + console.log("width:", d[0]); + return width; + }).attr("height", this.plot_height - this.y_buffer - 3).attr("fill", function(d, i) { + if ((i + 1) % 2) { + return "none"; } else { - return _this.x_scale(d[1]); + return "whitesmoke"; } - }).attr("y", this.y_buffer).attr("width", function(d) { - return _this.x_scale(d[0]); - }).attr("height", this.plot_height - this.y_buffer).attr("fill", function(d, i) { - return "whitesmoke"; }); }; @@ -316,7 +308,7 @@ } }).attr("x", function(d) { return _this.x_scale(d[2] - d[1] / 2); - }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "black").on("click", function(d) { + }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("cursor", "pointer").attr("fill", "black").on("click", function(d) { var this_chr; this_chr = d; return _this.redraw_plot(d); @@ -329,18 +321,44 @@ return _this.x_scale(d[0]); }).attr("cy", function(d) { return _this.y_scale(d[1]); - }).attr("r", 2).attr("id", function(d) { + }).attr("r", function(d) { + if (d[1] > 2) { + return 3; + } else { + return 2; + } + }).attr("fill", function(d) { + if (d[1] > 2) { + return "white"; + } else { + return "black"; + } + }).attr("stroke", "black").attr("stroke-width", "1").attr("id", function(d) { return "point_" + String(d[2]); }).classed("circle", true).on("mouseover", function(d) { var this_id; console.log("d3.event is:", d3.event); console.log("d is:", d); this_id = "point_" + String(d[2]); - return d3.select("#" + this_id).classed("d3_highlight", true).attr("r", 5).attr("fill", "yellow").call(_this.show_marker_in_table(d)); + return d3.select("#" + this_id).classed("d3_highlight", true).attr("r", 5).attr("stroke", "none").attr("fill", "blue").call(_this.show_marker_in_table(d)); }).on("mouseout", function(d) { var this_id; this_id = "point_" + String(d[2]); - return d3.select("#" + this_id).classed("d3_highlight", false).attr("r", 2).attr("fill", "black"); + return d3.select("#" + this_id).classed("d3_highlight", false).attr("r", function(d) { + if (d[1] > 2) { + return 3; + } else { + return 2; + } + }).attr("fill", function(d) { + if (d[1] > 2) { + return "white"; + } else { + return "black"; + } + }).attr("stroke", "black").attr("stroke-width", "1"); + }).append("svg:title").text(function(d) { + return d[2]; }); }; @@ -369,6 +387,8 @@ })(); - root.Manhattan_Plot = new Manhattan_Plot(600, 1200); + root.Manhattan_Plot = Manhattan_Plot; + + new Manhattan_Plot(600, 1200); }).call(this); diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 7f588e84..d826b63e 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -2,16 +2,24 @@ {% block title %}View Collection{% endblock %} {% block content %} <!-- Start of body --> - {{ header(uc.name, - 'This collection has {}.'.format(numify(trait_obs|count, "record", "records"))) }} - + {% if uc %} + {{ header(uc.name, + 'This collection has {}.'.format(numify(trait_obs|count, "record", "records"))) }} + {% else %} + {{ header('Your Collection', + 'This collection has {}.'.format(numify(trait_obs|count, "record", "records"))) }} + {% endif %} <div class="container"> <div class="page-header"> <h1>Your Collection</h1> + {% if uc %} <h2>{{ uc.name }}</h2> + {% endif %} <form action="/collections/delete" method="post"> + {% if uc %} <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" /> + {% endif %} <input type="submit" class="btn btn-small btn-danger" value="Delete this collection" /> diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html index 05fb9845..e05e45fd 100644 --- a/wqflask/wqflask/templates/marker_regression.html +++ b/wqflask/wqflask/templates/marker_regression.html @@ -73,8 +73,8 @@ <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/marker_regression.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_manhattan_plot.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/marker_regression.js"></script> <script type="text/javascript" charset="utf-8"> |