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-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py2
-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.coffee124
-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.js111
3 files changed, 123 insertions, 114 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 52870d84..9bf97f93 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -471,7 +471,7 @@ class MarkerRegression(object):
suggestive_results = []
self.pure_qtl_results = []
for result in self.qtl_results:
- self.pure_qtl_results.append(dict(locus=dict(cM=result.locus.cM,
+ self.pure_qtl_results.append(dict(locus=dict(mb=result.locus.Mb,
chromosome=result.locus.chr),
lrs=result.lrs,
additive=result.additive))
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index f3485a82..7ffa0267 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -2,68 +2,76 @@ $ ->
sort_number = (a, b) ->
return a - b
- process_lrs_array = ->
- # Put the data in a format needed for graphing
- # The permutation count for a particular integer range (10-11 or 12-13 for example)
- # will be on the y-axis; LRS values will be on the x-axis
- lrs_array = js_data.lrs_array
- bars = {}
- for lrs in lrs_array
- floored = Math.floor(lrs)
- if floored not of bars
- bars[floored] = 0
- bars[floored] += 1
- # Now we need to take the unordered hash
- # And order the keys
- keys = []
- for key of bars
- keys.push(key)
- keys.sort(sort_number)
+ process_lrs_array = ->
+ # Put the data in a format needed for graphing
+ # The permutation count for a particular integer range (10-11 or 12-13 for example)
+ # will be on the y-axis; LRS values will be on the x-axis
+ lrs_array = js_data.lrs_array
+ bars = {}
+ for lrs in lrs_array
+ floored = Math.floor(lrs)
+ if floored not of bars
+ bars[floored] = 0
+ bars[floored] += 1
+
+ # Now we need to take the unordered hash
+ # And order the keys
+ keys = []
+ for key of bars
+ keys.push(key)
-
- # Now that we have the ordered keys above
- # We can build an array of arrays that jqPlot will use
- bars_ordered = []
- for key in keys
- bars_ordered.push([parseInt(key), bars[key]])
-
- console.log("bars is:", bars)
- console.log("keys are:", keys)
- console.log("bars_ordered are:", bars_ordered)
- return bars_ordered
-
- display_permutation_histogram = (bars_ordered) ->
- # Figure out the largest key, so we can make sure the x axis max is one larger later on
- max_lrs = bars_ordered[bars_ordered.length-1][0]
- console.log("max_key is:", max_lrs)
+ keys.sort(sort_number)
+
+
+ # Now that we have the ordered keys above
+ # We can build an array of arrays that jqPlot will use
+ bars_ordered = []
+ for key in keys
+ bars_ordered.push([parseInt(key), bars[key]])
- $.jqplot('permutation_histogram', [bars_ordered],
- title: 'Permutation Histogram'
- seriesDefaults:
- renderer:$.jqplot.BarRenderer
- rendererOptions:
- #barPadding: 30
- #barMargin: 30
- barWidth: 15
- #shadowOffset: 2
- #shadowDepth: 5
- #shadowAlpha: 0.8
- pointLabels:
- show: true
- axesDefaults:
- labelRenderer: $.jqplot.CanvasAxisLabelRenderer
- axes:
- xaxis:
- min: 0
- #max: max_lrs + 2
- label: "LRS"
- pad: 1.1
- yaxis:
- min: 0
- label: "Frequency"
- )
+ console.log("bars is:", bars)
+ console.log("keys are:", keys)
+ console.log("bars_ordered are:", bars_ordered)
+ return bars_ordered
+
+ display_permutation_histogram = (bars_ordered) ->
+ # Figure out the largest key, so we can make sure the x axis max is one larger later on
+ max_lrs = bars_ordered[bars_ordered.length-1][0]
+ console.log("max_key is:", max_lrs)
+
+ $.jqplot('permutation_histogram', [bars_ordered],
+ title: 'Permutation Histogram'
+ seriesDefaults:
+ renderer:$.jqplot.BarRenderer
+ rendererOptions:
+ #barPadding: 30
+ #barMargin: 30
+ barWidth: 15
+ #shadowOffset: 2
+ #shadowDepth: 5
+ #shadowAlpha: 0.8
+ pointLabels:
+ show: true
+ axesDefaults:
+ labelRenderer: $.jqplot.CanvasAxisLabelRenderer
+ axes:
+ xaxis:
+ min: 0
+ #max: max_lrs + 2
+ label: "LRS"
+ pad: 1.1
+ yaxis:
+ min: 0
+ label: "Frequency"
+ )
+
+ #process_qtl_results = ->
+ # qtl_results = js_data.qtl_results
+
+ #display_manhattan_plot = ->
+
bars_ordered = process_lrs_array()
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index ac85dc3d..5d429ddc 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -2,67 +2,68 @@
(function() {
$(function() {
- var bars_ordered, display_permutation_histogram, process_lrs_array, sort_number;
+ var bars_ordered, sort_number;
sort_number = function(a, b) {
+ var display_permutation_histogram, process_lrs_array;
return a - b;
- };
- process_lrs_array = function() {
- var bars, bars_ordered, floored, key, keys, lrs, lrs_array, _i, _j, _len, _len1;
- lrs_array = js_data.lrs_array;
- bars = {};
- for (_i = 0, _len = lrs_array.length; _i < _len; _i++) {
- lrs = lrs_array[_i];
- floored = Math.floor(lrs);
- if (!(floored in bars)) {
- bars[floored] = 0;
+ process_lrs_array = function() {
+ var bars, bars_ordered, floored, key, keys, lrs, lrs_array, _i, _j, _len, _len1;
+ lrs_array = js_data.lrs_array;
+ bars = {};
+ for (_i = 0, _len = lrs_array.length; _i < _len; _i++) {
+ lrs = lrs_array[_i];
+ floored = Math.floor(lrs);
+ if (!(floored in bars)) {
+ bars[floored] = 0;
+ }
+ bars[floored] += 1;
}
- bars[floored] += 1;
- }
- keys = [];
- for (key in bars) {
- keys.push(key);
- }
- keys.sort(sort_number);
- bars_ordered = [];
- for (_j = 0, _len1 = keys.length; _j < _len1; _j++) {
- key = keys[_j];
- bars_ordered.push([parseInt(key), bars[key]]);
- }
- console.log("bars is:", bars);
- console.log("keys are:", keys);
- console.log("bars_ordered are:", bars_ordered);
- return bars_ordered;
- };
- display_permutation_histogram = function(bars_ordered) {
- var max_lrs;
- max_lrs = bars_ordered[bars_ordered.length - 1][0];
- console.log("max_key is:", max_lrs);
- return $.jqplot('permutation_histogram', [bars_ordered], {
- title: 'Permutation Histogram',
- seriesDefaults: {
- renderer: $.jqplot.BarRenderer,
- rendererOptions: {
- barWidth: 15
+ keys = [];
+ for (key in bars) {
+ keys.push(key);
+ }
+ keys.sort(sort_number);
+ bars_ordered = [];
+ for (_j = 0, _len1 = keys.length; _j < _len1; _j++) {
+ key = keys[_j];
+ bars_ordered.push([parseInt(key), bars[key]]);
+ }
+ console.log("bars is:", bars);
+ console.log("keys are:", keys);
+ console.log("bars_ordered are:", bars_ordered);
+ return bars_ordered;
+ };
+ return display_permutation_histogram = function(bars_ordered) {
+ var max_lrs;
+ max_lrs = bars_ordered[bars_ordered.length - 1][0];
+ console.log("max_key is:", max_lrs);
+ return $.jqplot('permutation_histogram', [bars_ordered], {
+ title: 'Permutation Histogram',
+ seriesDefaults: {
+ renderer: $.jqplot.BarRenderer,
+ rendererOptions: {
+ barWidth: 15
+ },
+ pointLabels: {
+ show: true
+ }
},
- pointLabels: {
- show: true
- }
- },
- axesDefaults: {
- labelRenderer: $.jqplot.CanvasAxisLabelRenderer
- },
- axes: {
- xaxis: {
- min: 0,
- label: "LRS",
- pad: 1.1
+ axesDefaults: {
+ labelRenderer: $.jqplot.CanvasAxisLabelRenderer
},
- yaxis: {
- min: 0,
- label: "Frequency"
+ axes: {
+ xaxis: {
+ min: 0,
+ label: "LRS",
+ pad: 1.1
+ },
+ yaxis: {
+ min: 0,
+ label: "Frequency"
+ }
}
- }
- });
+ });
+ };
};
bars_ordered = process_lrs_array();
return display_permutation_histogram(bars_ordered);