From 151c4614afe8c291b3154851aea9f5d670fe4efa Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 5 Dec 2013 22:54:18 +0000
Subject: Interval map graph now works properly
Tried to export trait data for "color by trait" function
---
wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 2 --
wqflask/wqflask/static/new/css/interval_mapping.css | 21 +++++++++++++--------
.../wqflask/static/new/css/marker_regression.css | 4 ++--
.../wqflask/static/new/javascript/bar_chart.coffee | 1 +
.../javascript/get_traits_from_collection.coffee | 9 +++++++--
.../new/javascript/get_traits_from_collection.js | 8 ++++++--
.../static/new/javascript/interval_mapping.coffee | 13 ++++++++-----
.../static/new/javascript/interval_mapping.js | 10 +++++-----
wqflask/wqflask/templates/collections/list.html | 2 +-
wqflask/wqflask/templates/show_trait.html | 4 +++-
10 files changed, 46 insertions(+), 28 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 6ef1669b..60d36b8d 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -107,8 +107,6 @@ def run_human(pheno_vector,
with Bench("Create list of inputs"):
inputs = list(plink_input)
-
- print("len(genotypes): ", len(inputs))
with Bench("Divide into chunks"):
results = chunks.divide_into_chunks(inputs, 64)
diff --git a/wqflask/wqflask/static/new/css/interval_mapping.css b/wqflask/wqflask/static/new/css/interval_mapping.css
index 9d23ba25..5ebf7742 100644
--- a/wqflask/wqflask/static/new/css/interval_mapping.css
+++ b/wqflask/wqflask/static/new/css/interval_mapping.css
@@ -1,27 +1,32 @@
-.manhattan_plot .y_axis path,
-.manhattan_plot .y_axis line {
+.interval_map .y_axis path,
+.interval_map .y_axis line {
fill: none;
stroke: black;
shape-rendering: crispEdges;
}
-.manhattan_plot .y_axis text {
+.interval_map .y_axis text {
font-family: sans-serif;
font-size: 14px;
}
-.manhattan_plot .x_axis path,
-.manhattan_plot .x_axis line {
+.interval_map .x_axis path,
+.interval_map .x_axis line {
fill: none;
stroke: black;
shape-rendering: crispEdges;
}
-.manhattan_plot .x_axis text {
+.interval_map .x_axis text {
text-anchor: end;
font-family: sans-serif;
font-size: 8px;
}
-rect {
+interval_map rect {
stroke: WhiteSmoke;
- fill: lightgrey;
+ fill: white;
+}
+
+interval_map path {
+ stroke: steelblue;
+ stroke-width: 1;
}
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css
index 054ef93e..a737c97e 100644
--- a/wqflask/wqflask/static/new/css/marker_regression.css
+++ b/wqflask/wqflask/static/new/css/marker_regression.css
@@ -21,10 +21,10 @@
font-size: 8px;
}
-rect {
+/*rect {
stroke: WhiteSmoke;
fill: lightgrey;
-}
+}*/
/*rect {
stroke: WhiteSmoke;
fill: Azure;
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.coffee b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
index 412185d8..d18cadd2 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
@@ -124,6 +124,7 @@ class Bar_Chart
d3.select("#color_by_trait").on("click", =>
@color_by_trait()
+
)
get_attr_color_dict: () ->
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee
index f1d41cbe..23499ac5 100644
--- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee
@@ -1,9 +1,11 @@
+root = exports ? this
console.log("before get_traits_from_collection")
# Going to be used to hold collection list
# So we can repopulate it when the back button is clicked
collection_list = null
+this_trait_data = null
collection_click = () ->
console.log("Clicking on:", $(this))
@@ -16,7 +18,7 @@ collection_click = () ->
url: this_collection_url,
success: process_traits
)
-
+
trait_click = () ->
console.log("Clicking on:", $(this))
trait = $(this).find('.trait').text()
@@ -30,7 +32,9 @@ trait_click = () ->
)
color_by_trait = (trait_sample_data, textStatus, jqXHR) ->
- console.log('in color_by_trait:', trait_sample_data)
+ root.trait_sample_data = trait_sample_data
+ #console.log('in color_by_trait:', trait_sample_data)
+
process_traits = (trait_data, textStatus, jqXHR) ->
console.log('in process_traits with trait_data:', trait_data)
@@ -65,3 +69,4 @@ $ ->
$(document).on("click", ".collection_line", collection_click)
$(document).on("click", ".trait_line", trait_click)
$(document).on("click", "#back_to_collections", back_to_collections)
+
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
index 104c411d..b4c2c200 100644
--- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
@@ -1,11 +1,15 @@
// Generated by CoffeeScript 1.6.1
(function() {
- var back_to_collections, collection_click, collection_list, color_by_trait, process_traits, trait_click;
+ var back_to_collections, collection_click, collection_list, color_by_trait, process_traits, root, this_trait_data, trait_click;
+
+ root = typeof exports !== "undefined" && exports !== null ? exports : this;
console.log("before get_traits_from_collection");
collection_list = null;
+ this_trait_data = null;
+
collection_click = function() {
var this_collection_url;
console.log("Clicking on:", $(this));
@@ -35,7 +39,7 @@
};
color_by_trait = function(trait_sample_data, textStatus, jqXHR) {
- return console.log('in color_by_trait:', trait_sample_data);
+ return root.trait_sample_data = trait_sample_data;
};
process_traits = function(trait_data, textStatus, jqXHR) {
diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.coffee b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
index 78265f27..0aa21d97 100644
--- a/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
+++ b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
@@ -215,10 +215,10 @@ $ ->
)
.enter()
.append("line")
- .attr("x1", @x_scale)
- .attr("x2", @x_scale)
.attr("y1", @y_buffer)
.attr("y2", @plot_height)
+ .attr("x1", @x_scale)
+ .attr("x2", @x_scale)
.style("stroke", "#ccc")
fill_chr_areas: () ->
@@ -239,7 +239,8 @@ $ ->
.attr("width", (d) =>
return @x_scale(d[0])
)
- .attr("height", @plot_height-@y_buffer)
+ .attr("height", @plot_height-@y_buffer)
+ .attr("fill", "white")
add_chr_labels: () ->
chr_names = []
@@ -263,12 +264,13 @@ $ ->
.attr("text-anchor", "middle")
.attr("font-family", "sans-serif")
.attr("font-size", "18px")
- .attr("fill", "grey")
+ #.attr("fill", "grey")
connect_markers: () ->
- @svg.selectAll("path")
+ @svg.selectAll("line")
.data(@plot_coordinates)
.enter()
+ .append("line")
.attr("x1", (d, i) =>
if i == 0
return @x_buffer
@@ -287,6 +289,7 @@ $ ->
.attr("y2", (d) =>
return @plot_height - ((@plot_height-@y_buffer) * d[1]/@y_max)
)
+ .style("stroke", "black")
console.time('Create manhattan plot')
new Interval_Map(600, 1200)
diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.js b/wqflask/wqflask/static/new/javascript/interval_mapping.js
index 5ae8ffab..521a1c7a 100644
--- a/wqflask/wqflask/static/new/javascript/interval_mapping.js
+++ b/wqflask/wqflask/static/new/javascript/interval_mapping.js
@@ -205,7 +205,7 @@
var _this = this;
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");
+ }).enter().append("line").attr("y1", this.y_buffer).attr("y2", this.plot_height).attr("x1", this.x_scale).attr("x2", this.x_scale).style("stroke", "#ccc");
};
Interval_Map.prototype.fill_chr_areas = function() {
@@ -220,7 +220,7 @@
}
}).attr("y", this.y_buffer).attr("width", function(d) {
return _this.x_scale(d[0]);
- }).attr("height", this.plot_height - this.y_buffer);
+ }).attr("height", this.plot_height - this.y_buffer).attr("fill", "white");
};
Interval_Map.prototype.add_chr_labels = function() {
@@ -237,12 +237,12 @@
return d[0];
}).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", "grey");
+ }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px");
};
Interval_Map.prototype.connect_markers = function() {
var _this = this;
- return this.svg.selectAll("path").data(this.plot_coordinates).enter().attr("x1", function(d, i) {
+ return this.svg.selectAll("line").data(this.plot_coordinates).enter().append("line").attr("x1", function(d, i) {
if (i === 0) {
return _this.x_buffer;
} else {
@@ -258,7 +258,7 @@
return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * d[0] / parseFloat(_this.x_max));
}).attr("y2", function(d) {
return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max);
- });
+ }).style("stroke", "black");
};
return Interval_Map;
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index ac621a61..354723d0 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -35,7 +35,7 @@
{# if "color_by_trait" in params #}
-
+
{# endif #}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index ec729e1c..0ad6eedb 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -2,6 +2,7 @@
{% block title %}Trait Data and Analysis{% endblock %}
{% block css %}
+
@@ -55,9 +56,10 @@
+
-
+
--
cgit v1.2.3