From be3c688ac3ddcc4f10a359bf68792e05dca63973 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 14 Apr 2016 21:19:12 +0000 Subject: Fixed issue where qtl lines in interval mapping wouldn't connect between chromosomes Added text explaining what * indicates in the mapping options menu Removed ranges (log2 and fold) from stats table for phenotype traits --- wqflask/wqflask/marker_regression/marker_regression_gn1.py | 8 +++----- wqflask/wqflask/search_results.py | 4 ++-- wqflask/wqflask/show_trait/show_trait.py | 9 +++++---- wqflask/wqflask/static/new/javascript/show_trait.js | 3 +++ wqflask/wqflask/templates/marker_regression_gn1.html | 9 ++++++--- wqflask/wqflask/templates/show_trait_statistics.html | 1 - 6 files changed, 19 insertions(+), 15 deletions(-) mode change 100755 => 100644 wqflask/wqflask/static/new/javascript/show_trait.js (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 63f62411..c10aac73 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -2015,6 +2015,9 @@ class MarkerRegression(object): thisLRSColor = self.colorCollection[0] if qtlresult['chr'] != previous_chr and self.selectedChr == -1: + if self.manhattan_plot != True: + canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + LRSCoordXY = [] previous_chr = qtlresult['chr'] previous_chr_as_int += 1 @@ -2032,7 +2035,6 @@ class MarkerRegression(object): else: this_chr = str(self.ChrList[self.selectedChr][1]+1) if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr: - #LRSCoordXY = [] #AdditiveCoordXY = [] #DominanceCoordXY = [] #for k, _locus in enumerate(_chr): @@ -2087,7 +2089,6 @@ class MarkerRegression(object): # Yc = yZero - qtlresult['dominance']*DominanceHeightThresh/dominanceMax # DominanceCoordXY.append((Xc, Yc)) m += 1 - #canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) lineWidth = 1 @@ -2151,9 +2152,6 @@ class MarkerRegression(object): canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - if self.manhattan_plot != True: - canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - ###draw additive scale if not self.multipleInterval and self.additiveChecked: additiveScaleFont=pid.Font(ttf="verdana",size=16*zoom,bold=0) diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index fb03f027..a57bfffe 100755 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -119,9 +119,9 @@ class SearchResultPage(object): #### Excel file needs to be generated #### - print("foo locals are:", locals()) + #print("foo locals are:", locals()) trait_id = result[0] - this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True) + this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) self.dataset.get_trait_info(self.trait_list, species) diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 3cc6121f..2d4c952a 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -152,10 +152,11 @@ class ShowTrait(object): self.trait_table_width = get_trait_table_width(self.sample_groups) - js_data = dict(sample_group_types = self.sample_group_types, - sample_lists = sample_lists, - attribute_names = self.sample_groups[0].attributes, - temp_uuid = self.temp_uuid) + js_data = dict(dataset_type = self.dataset.type, + sample_group_types = self.sample_group_types, + sample_lists = sample_lists, + attribute_names = self.sample_groups[0].attributes, + temp_uuid = self.temp_uuid) self.js_data = js_data def get_mapping_methods(self): diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js old mode 100755 new mode 100644 index 8d5982b7..663f7f3b --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -186,6 +186,9 @@ the_rows = ""; for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) { row = Stat_Table_Rows[_i]; + if ((row.vn == "range_fold" || row.vn == "range") && js_data.dataset_type == "Publish"){ + continue; + } console.log("rowing"); row_line = ""; if (row.url != null) { diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index d7950754..c65948c0 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -87,8 +87,8 @@ - -
+
+
{% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %} Permutation Test @@ -121,7 +121,10 @@ {% if plotScale != "morgan" %} Haplotype Analyst * {% endif %} -
+ +
+ * only apply to single chromosome physical mapping +
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 2183dd30..9c5c94b2 100755 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -27,7 +27,6 @@
-
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