From bab4e72f657eef01934dc7a1645dce6d3035c3fd Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 1 Jul 2021 18:41:45 +0000 Subject: Fixed bug where there'd be an error if the max boot count is 0 for a chromosome --- wqflask/wqflask/marker_regression/display_mapping_results.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index ec17d3b0..2d74ea52 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -861,6 +861,9 @@ class DisplayMappingResults: (item[1], yZero - item[2] * bootHeightThresh / maxBootCount)), fill=self.BOOTSTRAP_BOX_COLOR, outline=BLACK) + if maxBootCount == 0: + return + # draw boot scale highestPercent = (maxBootCount * 100.0) / nboot bootScale = Plot.detScale(0, highestPercent) -- cgit 1.4.1 From 323c52ff746dab78a2edc343958a81e0ac1b22a5 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 1 Jul 2021 20:59:47 +0000 Subject: Fixed issue where zooming into chromosome 1 was causing the Y axis scaling to be bad --- .../marker_regression/display_mapping_results.py | 17 +++-------------- 1 file changed, 3 insertions(+), 14 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 2d74ea52..dfae4065 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2289,20 +2289,9 @@ class DisplayMappingResults: font=VERDANA_FILE, size=int(18 * zoom * 1.5)) yZero = yTopOffset + plotHeight - # LRSHeightThresh = drawAreaHeight - # AdditiveHeightThresh = drawAreaHeight/2 - # DominanceHeightThresh = drawAreaHeight/2 - if self.selectedChr == 1: - LRSHeightThresh = drawAreaHeight - yTopOffset + 30 * (zoom - 1) - AdditiveHeightThresh = LRSHeightThresh / 2 - DominanceHeightThresh = LRSHeightThresh / 2 - else: - LRSHeightThresh = drawAreaHeight - AdditiveHeightThresh = drawAreaHeight / 2 - DominanceHeightThresh = drawAreaHeight / 2 - # LRSHeightThresh = (yZero - yTopOffset + 30*(zoom - 1)) - # AdditiveHeightThresh = LRSHeightThresh/2 - # DominanceHeightThresh = LRSHeightThresh/2 + LRSHeightThresh = drawAreaHeight + AdditiveHeightThresh = drawAreaHeight / 2 + DominanceHeightThresh = drawAreaHeight / 2 if LRS_LOD_Max > 100: LRSScale = 20.0 -- cgit 1.4.1 From d4c990beaf72dd885d6baa7dc1035a7044c79cdd Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 1 Jul 2021 21:28:10 +0000 Subject: Fixed issue where the interval map QTL line might extend beyond the graph edge when zoomed into a Mb range + removed some commented out code --- .../marker_regression/display_mapping_results.py | 20 +++++++------------- 1 file changed, 7 insertions(+), 13 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index dfae4065..1fcc2832 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2561,7 +2561,10 @@ class DisplayMappingResults: Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * ( ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale)) else: - Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale + if qtlresult['Mb'] > endMb: + Xc = startPosX + endMb * plotXScale + else: + Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale # updated by NL 06-18-2011: # fix the over limit LRS graph issue since genotype trait may give infinite LRS; @@ -2572,36 +2575,29 @@ class DisplayMappingResults: if 'lrs_value' in qtlresult: if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP": if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': - #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) Yc = yZero - webqtlConfig.MAXLRS * \ LRSHeightThresh / \ (LRS_LOD_Max * self.LODFACTOR) else: - #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) Yc = yZero - \ qtlresult['lrs_value'] * LRSHeightThresh / \ (LRS_LOD_Max * self.LODFACTOR) else: if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': - #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max else: - #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - \ qtlresult['lrs_value'] * \ LRSHeightThresh / LRS_LOD_Max else: if qtlresult['lod_score'] > 100 or qtlresult['lod_score'] == 'inf': - #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max else: if self.LRS_LOD == "LRS": - #Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - \ qtlresult['lod_score'] * self.LODFACTOR * \ LRSHeightThresh / LRS_LOD_Max else: - #Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - \ qtlresult['lod_score'] * \ LRSHeightThresh / LRS_LOD_Max @@ -2634,14 +2630,12 @@ class DisplayMappingResults: AdditiveHeightThresh / additiveMax AdditiveCoordXY.append((Xc, Yc)) + if qtlresult['Mb'] > endMb: + break + m += 1 if self.manhattan_plot != True: - # im_drawer.polygon( - # xy=LRSCoordXY, - # outline=thisLRSColor - # #, closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth) - # ) draw_open_polygon(canvas, xy=LRSCoordXY, outline=thisLRSColor, width=lrsEdgeWidth) -- cgit 1.4.1 From 74c1d6a6ef070271adaf486fc9a494662855d96f Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 1 Jul 2021 21:40:24 +0000 Subject: Fixed issue with suggestive/significant lines extending beyond figure edge + fixed a couple issues with the last commit --- wqflask/wqflask/marker_regression/display_mapping_results.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 1fcc2832..f941267e 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2372,8 +2372,7 @@ class DisplayMappingResults: # ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist): - rightEdge = int(start_pos_x + chr_length_dist * \ - plotXScale - self.SUGGESTIVE_WIDTH / 1.5) + rightEdge = xLeftOffset + plotWidth im_drawer.line( xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, suggestiveY), (rightEdge, suggestiveY)), @@ -2561,7 +2560,7 @@ class DisplayMappingResults: Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * ( ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale)) else: - if qtlresult['Mb'] > endMb: + if self.selectedChr != -1 and qtlresult['Mb'] > endMb: Xc = startPosX + endMb * plotXScale else: Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale @@ -2630,7 +2629,7 @@ class DisplayMappingResults: AdditiveHeightThresh / additiveMax AdditiveCoordXY.append((Xc, Yc)) - if qtlresult['Mb'] > endMb: + if self.selectedChr != -1 and qtlresult['Mb'] > endMb: break m += 1 -- cgit 1.4.1