diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 15 |
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): |