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-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.coffee56
-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.js50
2 files changed, 66 insertions, 40 deletions
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 2b09fbc8..4b0915c2 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -12,16 +12,14 @@ $ ->
@y_coords = []
@marker_names = []
@create_coordinates()
- @scaled_chr_lengths = @get_chr_lengths()
+ [@chr_lengths, @cumulative_chr_lengths] = @get_chr_lengths()
# Buffer to allow for the ticks/labels to be drawn
- @x_buffer = @plot_width/25
+ @x_buffer = @plot_width/30
@y_buffer = @plot_height/20
#@x_max = d3.max(@x_coords)
- console.log("x_max is", d3.max(@x_coords))
@x_max = @total_length
- console.log("x_max is", @x_max)
@y_max = d3.max(@y_coords) * 1.2
@svg = @create_svg()
@@ -42,22 +40,24 @@ $ ->
get_chr_lengths: () ->
###
- Gets a list of cumulative lengths in order to draw the vertical
- lines separating chromosomes (the position of one on the graph is its own length
- plus the lengths of all preceding chromosomes)
+ Gets a list of both individual and cumulative (the position of one on the graph
+ is its own length plus the lengths of all preceding chromosomes) lengths in order
+ to draw the vertical lines separating chromosomes and the chromosome labels
###
cumulative_chr_lengths = []
+ chr_lengths = []
total_length = 0
for key of @chromosomes
this_length = @chromosomes[key]
+ chr_lengths.push(this_length)
cumulative_chr_lengths.push(total_length + this_length)
total_length += this_length
console.log("total length is:", total_length)
- return cumulative_chr_lengths
+ return [chr_lengths, cumulative_chr_lengths]
create_coordinates: () ->
chr_lengths = []
@@ -85,9 +85,6 @@ $ ->
else
marker_name = ""
$("#qtl_results_filter").find("input:first").val(marker_name).keyup()
-
- #unselect_marker: () ->
- # $("#qtl_results_filter").find("input:first").val("").keyup()
create_svg: () ->
svg = d3.select("#manhattan_plots")
@@ -97,15 +94,6 @@ $ ->
return svg
- create_scales: () ->
- @x_scale = d3.scale.linear()
- .domain([0, d3.max(@x_coords)])
- .range([@x_buffer, @plot_width])
-
- @y_scale = d3.scale.linear()
- .domain([0, @y_max])
- .range([@plot_height, @y_buffer])
-
create_graph: () ->
@add_border()
@add_y_axis()
@@ -136,6 +124,16 @@ $ ->
)
.style("stroke", "#000")
+ create_scales: () ->
+ console.log("plot_width is: ", @plot_width)
+ @x_scale = d3.scale.linear()
+ .domain([0, d3.max(@x_coords)])
+ .range([@x_buffer, @plot_width])
+
+ @y_scale = d3.scale.linear()
+ .domain([0, @y_max])
+ .range([@plot_height, @y_buffer])
+
add_y_axis: () ->
yAxis = d3.svg.axis()
.scale(@y_scale)
@@ -149,7 +147,7 @@ $ ->
add_chr_lines: () ->
@svg.selectAll("line")
- .data(@scaled_chr_lengths, (d) =>
+ .data(@cumulative_chr_lengths, (d) =>
return d
)
.enter()
@@ -159,18 +157,30 @@ $ ->
.attr("y1", @y_buffer)
.attr("y2", @plot_height)
.style("stroke", "#ccc")
+
+ add_chr_labels: () ->
+ @svg.selectAll("text")
+ .data(_.zip(@chr_lengths, @cumulative_chr_lengths), (d) =>
+ label_positions = []
+ for chr in d
+ label_positions.push(chr[1] - chr[0]/2)
+ return label_positions
+ )
+ .enter()
+ .append("text")
add_plot_points: () ->
+ console.log("x_max is:", @x_max)
@svg.selectAll("circle")
.data(@plot_coordinates)
.enter()
.append("circle")
.attr("cx", (d) =>
- return @x_buffer + (@plot_width * d[0]/@x_max)
+ return @x_buffer + ((@plot_width-@x_buffer) * d[0]/@x_max)
)
.attr("cy", (d) =>
- return @plot_height - ((@plot_height) * d[1]/@y_max)
+ return @plot_height - ((@plot_height-@y_buffer) * d[1]/@y_max)
)
.attr("r", 2)
.classed("circle", true)
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index 38d88208..a1c73913 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -7,6 +7,7 @@
Manhattan_Plot = (function() {
function Manhattan_Plot(plot_height, plot_width) {
+ var _ref;
this.plot_height = plot_height;
this.plot_width = plot_width;
this.qtl_results = js_data.qtl_results;
@@ -17,12 +18,10 @@
this.y_coords = [];
this.marker_names = [];
this.create_coordinates();
- this.scaled_chr_lengths = this.get_chr_lengths();
- this.x_buffer = this.plot_width / 25;
+ _ref = this.get_chr_lengths(), this.chr_lengths = _ref[0], this.cumulative_chr_lengths = _ref[1];
+ this.x_buffer = this.plot_width / 30;
this.y_buffer = this.plot_height / 20;
- console.log("x_max is", d3.max(this.x_coords));
this.x_max = this.total_length;
- console.log("x_max is", this.x_max);
this.y_max = d3.max(this.y_coords) * 1.2;
this.svg = this.create_svg();
this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
@@ -50,21 +49,23 @@
Manhattan_Plot.prototype.get_chr_lengths = function() {
/*
- Gets a list of cumulative lengths in order to draw the vertical
- lines separating chromosomes (the position of one on the graph is its own length
- plus the lengths of all preceding chromosomes)
+ Gets a list of both individual and cumulative (the position of one on the graph
+ is its own length plus the lengths of all preceding chromosomes) lengths in order
+ to draw the vertical lines separating chromosomes and the chromosome labels
*/
- var cumulative_chr_lengths, key, this_length, total_length;
+ var chr_lengths, cumulative_chr_lengths, key, this_length, total_length;
cumulative_chr_lengths = [];
+ chr_lengths = [];
total_length = 0;
for (key in this.chromosomes) {
this_length = this.chromosomes[key];
+ chr_lengths.push(this_length);
cumulative_chr_lengths.push(total_length + this_length);
total_length += this_length;
}
console.log("total length is:", total_length);
- return cumulative_chr_lengths;
+ return [chr_lengths, cumulative_chr_lengths];
};
Manhattan_Plot.prototype.create_coordinates = function() {
@@ -111,11 +112,6 @@
return svg;
};
- Manhattan_Plot.prototype.create_scales = function() {
- this.x_scale = d3.scale.linear().domain([0, d3.max(this.x_coords)]).range([this.x_buffer, this.plot_width]);
- return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
- };
-
Manhattan_Plot.prototype.create_graph = function() {
this.add_border();
this.add_y_axis();
@@ -138,6 +134,12 @@
}).style("stroke", "#000");
};
+ Manhattan_Plot.prototype.create_scales = function() {
+ console.log("plot_width is: ", this.plot_width);
+ this.x_scale = d3.scale.linear().domain([0, d3.max(this.x_coords)]).range([this.x_buffer, this.plot_width]);
+ return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
+ };
+
Manhattan_Plot.prototype.add_y_axis = function() {
var yAxis;
yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
@@ -146,17 +148,31 @@
Manhattan_Plot.prototype.add_chr_lines = function() {
var _this = this;
- return this.svg.selectAll("line").data(this.scaled_chr_lengths, function(d) {
+ return this.svg.selectAll("line").data(this.cumulative_chr_lengths, function(d) {
return d;
}).enter().append("line").attr("x1", this.x_scale).attr("x2", this.x_scale).attr("y1", this.y_buffer).attr("y2", this.plot_height).style("stroke", "#ccc");
};
+ Manhattan_Plot.prototype.add_chr_labels = function() {
+ var _this = this;
+ return this.svg.selectAll("text").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), function(d) {
+ var chr, label_positions, _i, _len;
+ label_positions = [];
+ for (_i = 0, _len = d.length; _i < _len; _i++) {
+ chr = d[_i];
+ label_positions.push(chr[1] - chr[0] / 2);
+ }
+ return label_positions;
+ }).enter().append("text");
+ };
+
Manhattan_Plot.prototype.add_plot_points = function() {
var _this = this;
+ console.log("x_max is:", this.x_max);
return this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", function(d) {
- return _this.x_buffer + (_this.plot_width * d[0] / _this.x_max);
+ return _this.x_buffer + ((_this.plot_width - _this.x_buffer) * d[0] / _this.x_max);
}).attr("cy", function(d) {
- return _this.plot_height - (_this.plot_height * d[1] / _this.y_max);
+ return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max);
}).attr("r", 2).classed("circle", true).on("mouseover", function(d) {
return d3.select(d3.event.target).classed("d3_highlight", true).attr("r", 5).attr("fill", "yellow").call(_this.show_marker_in_table(d));
}).on("mouseout", function() {
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 20:46:38 +0000