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authorzsloan2016-08-24 21:19:13 +0000
committerzsloan2016-08-24 21:19:13 +0000
commit5ad7e4634f2e8b5cc5b10442da2dd80385e9aee6 (patch)
tree4ac62de1b95987c707629c3ab5126be28e0a29d3
parent4695840f6100d566c251eaa09498a60f6d7cfe29 (diff)
downloadgenenetwork2-5ad7e4634f2e8b5cc5b10442da2dd80385e9aee6.tar.gz
Fixed issue causing bootstrap results to not plot correctly.
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py3
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py15
2 files changed, 10 insertions, 8 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index a53afd5a..f3b018b8 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -213,7 +213,6 @@ class MarkerRegression(object):
if 'lod_score' in marker.keys():
self.qtl_results.append(marker)
-
self.trimmed_markers = results
for qtl in enumerate(self.qtl_results):
@@ -242,7 +241,7 @@ class MarkerRegression(object):
highest_chr = marker['chr']
if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
self.qtl_results.append(marker)
-
+
self.trimmed_markers = trim_markers_for_table(results)
self.json_data['chr'] = []
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index f902afb7..3db5b0f6 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -211,6 +211,8 @@ class MarkerRegression(object):
self.plotScale = start_vars['mapping_scale']
else:
self.plotScale = "physic"
+
+ self.manhattan_plot = start_vars['manhattan_plot']
if 'permCheck' in start_vars.keys():
self.permChecked = start_vars['permCheck']
@@ -261,6 +263,8 @@ class MarkerRegression(object):
self.strainlist = self.dataset.group.samplelist
self.genotype = self.dataset.group.read_genotype_file()
+ if self.mapping_method == "reaper" and self.manhattan_plot != True:
+ self.genotype = self.genotype.addinterval()
#Darwing Options
try:
@@ -283,7 +287,6 @@ class MarkerRegression(object):
## END HaplotypeAnalyst
self.graphHeight = self.GRAPH_DEFAULT_HEIGHT
- self.manhattan_plot = start_vars['manhattan_plot']
self.dominanceChecked = False
self.LRS_LOD = start_vars['LRSCheck']
self.cutoff = start_vars['cutoff']
@@ -809,8 +812,8 @@ class MarkerRegression(object):
plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
#draw bootstap
- #if self.bootChecked and not self.multipleInterval:
- # self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+ if self.bootChecked and not self.multipleInterval and not self.manhattan_plot:
+ self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
# Draw clickable region and gene band if selected
if self.plotScale == 'physic' and self.selectedChr > -1:
@@ -880,8 +883,8 @@ class MarkerRegression(object):
else:
Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale
BootCoord[-1].append([Xc, self.bootResult[i]])
- i += 1
-
+ i += 1
+
#reduce bootResult
if self.selectedChr > -1:
maxBootBar = 80.0
@@ -2023,7 +2026,7 @@ class MarkerRegression(object):
if self.manhattan_plot != True:
canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- if not self.multipleInterval and self.additiveChecked:
+ if not self.multipleInterval and not self.manhattan_plot and self.additiveChecked:
plusColor = self.ADDITIVE_COLOR_POSITIVE
minusColor = self.ADDITIVE_COLOR_NEGATIVE
for k, aPoint in enumerate(AdditiveCoordXY):