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| author | zsloan | 2016-03-21 20:23:59 +0000 |
|---|---|---|
| committer | zsloan | 2016-03-21 20:23:59 +0000 |
| commit | a65a5e0ff16e033dd8a67808711663851afd0169 (patch) | |
| tree | 2a0263308d9e7e7f4844ef5b669bac8257bed963 | |
| parent | 857d6d36a7e97b398c007083b7c5c05a44430bcb (diff) | |
| download | genenetwork2-a65a5e0ff16e033dd8a67808711663851afd0169.tar.gz | |
Manhattan plot option now works for GN1 map, and GEMMA is set to display as manhattan plot
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 12 |
2 files changed, 10 insertions, 3 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index b75a30f6..c50b9d78 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -91,6 +91,7 @@ class MarkerRegression(object): self.dataset.group.get_markers() if self.mapping_method == "gemma": self.score_type = "LOD" + self.manhattan_plot = True with Bench("Running GEMMA"): included_markers, p_values = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals) with Bench("Getting markers from csv"): diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index e9052290..01cee4f4 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -285,6 +285,7 @@ class MarkerRegression(object): self.graphHeight = self.GRAPH_DEFAULT_HEIGHT + self.manhattan_plot = start_vars['manhattan_plot'] self.additiveChecked = False self.dominanceChecked = False self.LRS_LOD = start_vars['score_type'] @@ -1989,7 +1990,11 @@ class MarkerRegression(object): #else: # Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax - LRSCoordXY.append((Xc, Yc)) + if self.manhattan_plot == True: + canvas.drawEllipse(Xc-1, Yc-1, Xc+1, Yc+1, fillColor=pid.black) + else: + LRSCoordXY.append((Xc, Yc)) + #if not self.multipleInterval and self.additiveChecked: # if additiveMax == 0.0: # additiveMax = 0.000001 @@ -1999,7 +2004,8 @@ class MarkerRegression(object): # Yc = yZero - qtlresult[m].dominance*DominanceHeightThresh/dominanceMax # DominanceCoordXY.append((Xc, Yc)) m += 1 - #canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + if self.manhattan_plot != True: + canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) lineWidth = 1 if not self.multipleInterval and self.additiveChecked: @@ -2062,7 +2068,7 @@ class MarkerRegression(object): canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + #canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) ###draw additive scale if not self.multipleInterval and self.additiveChecked: |