diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 185 |
1 files changed, 103 insertions, 82 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 9ac4946b..25846099 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -27,7 +27,7 @@ import datetime import string from math import * -import piddle as pid +from PIL import (ImageColor) import sys,os import cPickle import httplib @@ -49,6 +49,27 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR import utility.logger logger = utility.logger.getLogger(__name__ ) +RED = ImageColor.getrgb("red") +BLUE = ImageColor.getrgb("blue") +GRAY = ImageColor.getrgb("gray") +GOLD = ImageColor.getrgb("gold") +BLACK = ImageColor.getrgb("black") +GREEN = ImageColor.getrgb("green") +PURPLE = ImageColor.getrgb("purple") +ORANGE = ImageColor.getrgb("orange") +YELLOW = ImageColor.getrgb("yellow") +DARKRED = ImageColor.getrgb("darkred") +DARKBLUE = ImageColor.getrgb("darkblue") +DARKGRAY = ImageColor.getrgb("darkgray") +DEEPPINK = ImageColor.getrgb("deeppink") +DARKGREEN = ImageColor.getrgb("darkgreen") +GAINSBORO = ImageColor.getrgb("gainsboro") +LIGHTBLUE = ImageColor.getrgb("lightblue") +DARKORANGE = ImageColor.getrgb("darkorange") +DARKVIOLET = ImageColor.getrgb("darkviolet") +MEDIUMPURPLE = ImageColor.getrgb("mediumpurple") +# ---- END: Define common colours ---- # + ######################################### # Inteval Mapping Plot Page ######################################### @@ -96,47 +117,47 @@ class DisplayMappingResults(object): LODFACTOR = 4.61 - SNP_COLOR = pid.orange # Color for the SNP "seismograph" - TRANSCRIPT_LOCATION_COLOR = pid.mediumpurple + SNP_COLOR = ORANGE # Color for the SNP "seismograph" + TRANSCRIPT_LOCATION_COLOR = MEDIUMPURPLE - BOOTSTRAP_BOX_COLOR = pid.yellow - LRS_COLOR = pid.HexColor(0x0000FF) - SIGNIFICANT_COLOR = pid.HexColor(0xEBC7C7) - SUGGESTIVE_COLOR = pid.gainsboro + BOOTSTRAP_BOX_COLOR = YELLOW + LRS_COLOR = ImageColor.getrgb("#0000FF") + SIGNIFICANT_COLOR = ImageColor.getrgb("#EBC7C7") + SUGGESTIVE_COLOR = GAINSBORO SIGNIFICANT_WIDTH = 5 SUGGESTIVE_WIDTH = 5 - ADDITIVE_COLOR_POSITIVE = pid.green - ADDITIVE_COLOR_NEGATIVE = pid.orange - DOMINANCE_COLOR_POSITIVE = pid.darkviolet - DOMINANCE_COLOR_NEGATIVE = pid.red + ADDITIVE_COLOR_POSITIVE = GREEN + ADDITIVE_COLOR_NEGATIVE = ORANGE + DOMINANCE_COLOR_POSITIVE = DARKVIOLET + DOMINANCE_COLOR_NEGATIVE = RED ## BEGIN HaplotypeAnalyst - HAPLOTYPE_POSITIVE = pid.green - HAPLOTYPE_NEGATIVE = pid.red - HAPLOTYPE_HETEROZYGOUS = pid.blue - HAPLOTYPE_RECOMBINATION = pid.darkgray + HAPLOTYPE_POSITIVE = GREEN + HAPLOTYPE_NEGATIVE = RED + HAPLOTYPE_HETEROZYGOUS = BLUE + HAPLOTYPE_RECOMBINATION = DARKGRAY ## END HaplotypeAnalyst - TOP_RIGHT_INFO_COLOR = pid.black + TOP_RIGHT_INFO_COLOR = BLACK - CLICKABLE_WEBQTL_REGION_COLOR = pid.HexColor(0xF5D3D3) - CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = pid.HexColor(0xFCE9E9) - CLICKABLE_WEBQTL_TEXT_COLOR = pid.HexColor(0x912828) + CLICKABLE_WEBQTL_REGION_COLOR = ImageColor.getrgb("#F5D3D3") + CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = ImageColor.getrgb("#FCE9E9") + CLICKABLE_WEBQTL_TEXT_COLOR = ImageColor.getrgb("#912828") - CLICKABLE_PHENOGEN_REGION_COLOR = pid.HexColor(0xA2FB94) - CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR = pid.HexColor(0xCEFEC7) - CLICKABLE_PHENOGEN_TEXT_COLOR = pid.HexColor(0x1FD504) + CLICKABLE_PHENOGEN_REGION_COLOR = ImageColor.getrgb("#A2FB94") + CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR = ImageColor.getrgb("#CEFEC7") + CLICKABLE_PHENOGEN_TEXT_COLOR = ImageColor.getrgb("#1FD504") - CLICKABLE_UCSC_REGION_COLOR = pid.HexColor(0xDDDDEE) - CLICKABLE_UCSC_REGION_OUTLINE_COLOR = pid.HexColor(0xEDEDFF) - CLICKABLE_UCSC_TEXT_COLOR = pid.HexColor(0x333366) + CLICKABLE_UCSC_REGION_COLOR = ImageColor.getrgb("#DDDDEE") + CLICKABLE_UCSC_REGION_OUTLINE_COLOR = ImageColor.getrgb("#EDEDFF") + CLICKABLE_UCSC_TEXT_COLOR = ImageColor.getrgb("#333366") - CLICKABLE_ENSEMBL_REGION_COLOR = pid.HexColor(0xEEEEDD) - CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR = pid.HexColor(0xFEFEEE) - CLICKABLE_ENSEMBL_TEXT_COLOR = pid.HexColor(0x555500) + CLICKABLE_ENSEMBL_REGION_COLOR = ImageColor.getrgb("#EEEEDD") + CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR = ImageColor.getrgb("#FEFEEE") + CLICKABLE_ENSEMBL_TEXT_COLOR = ImageColor.getrgb("#555500") - GRAPH_BACK_LIGHT_COLOR = pid.HexColor(0xFBFBFF) - GRAPH_BACK_DARK_COLOR = pid.HexColor(0xF1F1F9) + GRAPH_BACK_LIGHT_COLOR = ImageColor.getrgb("#FBFBFF") + GRAPH_BACK_DARK_COLOR = ImageColor.getrgb("#F1F1F9") HELP_PAGE_REF = '/glossary.html' @@ -698,23 +719,23 @@ class DisplayMappingResults(object): bootOffset = 50*fontZoom bootScaleFont=pid.Font(ttf="verdana",size=13*fontZoom,bold=0) - canvas.drawRect(canvas.size[0]-bootOffset,yZero-bootHeightThresh,canvas.size[0]-bootOffset-15*zoom,yZero,fillColor = pid.yellow) - canvas.drawLine(canvas.size[0]-bootOffset+4, yZero, canvas.size[0]-bootOffset, yZero, color=pid.black) - canvas.drawString('0%' ,canvas.size[0]-bootOffset+10,yZero+5,font=bootScaleFont,color=pid.black) + canvas.drawRect(canvas.size[0]-bootOffset,yZero-bootHeightThresh,canvas.size[0]-bootOffset-15*zoom,yZero,fillColor = YELLOW) + canvas.drawLine(canvas.size[0]-bootOffset+4, yZero, canvas.size[0]-bootOffset, yZero, color=BLACK) + canvas.drawString('0%' ,canvas.size[0]-bootOffset+10,yZero+5,font=bootScaleFont,color=BLACK) for item in bootScale: if item == 0: continue bootY = yZero-bootHeightThresh*item/highestPercent - canvas.drawLine(canvas.size[0]-bootOffset+4,bootY,canvas.size[0]-bootOffset,bootY,color=pid.black) - canvas.drawString('%2.1f'%item ,canvas.size[0]-bootOffset+10,bootY+5,font=bootScaleFont,color=pid.black) + canvas.drawLine(canvas.size[0]-bootOffset+4,bootY,canvas.size[0]-bootOffset,bootY,color=BLACK) + canvas.drawString('%2.1f'%item ,canvas.size[0]-bootOffset+10,bootY+5,font=bootScaleFont,color=BLACK) if self.legendChecked: startPosY = 30 nCol = 2 smallLabelFont = pid.Font(ttf="trebuc", size=12*fontZoom, bold=1) leftOffset = xLeftOffset+(nCol-1)*200 - canvas.drawRect(leftOffset,startPosY-6, leftOffset+12,startPosY+6, fillColor=pid.yellow) - canvas.drawString('Frequency of the Peak LRS',leftOffset+ 20, startPosY+5,font=smallLabelFont,color=pid.black) + canvas.drawRect(leftOffset,startPosY-6, leftOffset+12,startPosY+6, fillColor=YELLOW) + canvas.drawString('Frequency of the Peak LRS',leftOffset+ 20, startPosY+5,font=smallLabelFont,color=BLACK) def drawProbeSetPosition(self, canvas, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): if len(self.traitList) != 1: @@ -784,7 +805,7 @@ class DisplayMappingResults(object): break if locPixel >= 0 and self.plotScale == 'physic': traitPixel = ((locPixel, yZero), (locPixel-7, yZero+14), (locPixel+7, yZero+14)) - canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) + canvas.drawPolygon(traitPixel, edgeColor=BLACK, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) if self.legendChecked: startPosY = 15 @@ -794,7 +815,7 @@ class DisplayMappingResults(object): leftOffset = xLeftOffset else: leftOffset = xLeftOffset+(nCol-1)*200*fontZoom - canvas.drawPolygon(((leftOffset+7, startPosY-7), (leftOffset, startPosY+7), (leftOffset+14, startPosY+7)), edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) + canvas.drawPolygon(((leftOffset+7, startPosY-7), (leftOffset, startPosY+7), (leftOffset+14, startPosY+7)), edgeColor=BLACK, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) canvas.drawString("Sequence Site", (leftOffset+15), (startPosY+5), smallLabelFont, self.TOP_RIGHT_INFO_COLOR) def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): @@ -863,7 +884,7 @@ class DisplayMappingResults(object): nameWidths.append(nameWidth) canvas.drawRect(rightShift,yPaddingTop+kstep*15, rectWidth+rightShift,yPaddingTop+10+kstep*15, fillColor=thisLRSColor) - canvas.drawString(name,rectWidth+2+rightShift,yPaddingTop+10+kstep*15,font=colorFont,color=pid.black) + canvas.drawString(name,rectWidth+2+rightShift,yPaddingTop+10+kstep*15,font=colorFont,color=BLACK) if thisTrait.db: COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,) HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name) @@ -884,21 +905,21 @@ class DisplayMappingResults(object): stepPosY = 12*fontZoom if self.manhattan_plot != True: canvas.drawLine(xLeftOffset,startPosY,xLeftOffset+32,startPosY,color=self.LRS_COLOR, width=2) - canvas.drawString(self.LRS_LOD, xLeftOffset+40,startPosY+5,font=labelFont,color=pid.black) + canvas.drawString(self.LRS_LOD, xLeftOffset+40,startPosY+5,font=labelFont,color=BLACK) startPosY += stepPosY if self.additiveChecked: startPosX = xLeftOffset canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.ADDITIVE_COLOR_POSITIVE, width=2) canvas.drawLine(startPosX+18,startPosY,startPosX+32,startPosY,color=self.ADDITIVE_COLOR_NEGATIVE, width=2) - canvas.drawString('Additive Effect',startPosX+40,startPosY+5,font=labelFont,color=pid.black) + canvas.drawString('Additive Effect',startPosX+40,startPosY+5,font=labelFont,color=BLACK) if self.genotype.type == 'intercross' and self.dominanceChecked: startPosX = xLeftOffset startPosY += stepPosY canvas.drawLine(startPosX,startPosY,startPosX+17,startPosY,color=self.DOMINANCE_COLOR_POSITIVE, width=4) canvas.drawLine(startPosX+18,startPosY,startPosX+35,startPosY,color=self.DOMINANCE_COLOR_NEGATIVE, width=4) - canvas.drawString('Dominance Effect',startPosX+42,startPosY+5,font=labelFont,color=pid.black) + canvas.drawString('Dominance Effect',startPosX+42,startPosY+5,font=labelFont,color=BLACK) if self.haplotypeAnalystChecked: startPosY += stepPosY @@ -907,18 +928,18 @@ class DisplayMappingResults(object): canvas.drawLine(startPosX+18,startPosY,startPosX+35,startPosY,color=self.HAPLOTYPE_NEGATIVE, width=4) canvas.drawLine(startPosX+36,startPosY,startPosX+53,startPosY,color=self.HAPLOTYPE_HETEROZYGOUS, width=4) canvas.drawLine(startPosX+54,startPosY,startPosX+67,startPosY,color=self.HAPLOTYPE_RECOMBINATION, width=4) - canvas.drawString('Haplotypes (Pat, Mat, Het, Unk)',startPosX+76,startPosY+5,font=labelFont,color=pid.black) + canvas.drawString('Haplotypes (Pat, Mat, Het, Unk)',startPosX+76,startPosY+5,font=labelFont,color=BLACK) if self.permChecked and self.nperm > 0: startPosY += stepPosY startPosX = xLeftOffset canvas.drawLine(startPosX, startPosY, startPosX + 32, startPosY, color=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH) canvas.drawLine(startPosX, startPosY + stepPosY, startPosX + 32, startPosY + stepPosY, color=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH) - canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significant),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black) - canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black) + canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significant),xLeftOffset+42,startPosY +5,font=labelFont,color=BLACK) + canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=BLACK) labelFont = pid.Font(ttf="verdana",size=12*fontZoom) - labelColor = pid.black + labelColor = BLACK if self.dataset.type == "Publish" or self.dataset.type == "Geno": dataset_label = self.dataset.fullname else: @@ -1042,19 +1063,19 @@ class DisplayMappingResults(object): densities=[1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0] if SNPdensity < densities[0]: - myColor = pid.black + myColor = BLACK elif SNPdensity < densities[1]: - myColor = pid.purple + myColor = PURPLE elif SNPdensity < densities[2]: - myColor = pid.darkblue + myColor = DARKBLUE elif SNPdensity < densities[3]: - myColor = pid.darkgreen + myColor = DARKGREEN elif SNPdensity < densities[4]: - myColor = pid.gold + myColor = GOLD elif SNPdensity < densities[5]: - myColor = pid.darkorange + myColor = DARKORANGE else: - myColor = pid.darkred + myColor = DARKRED outlineColor = myColor fillColor = myColor @@ -1086,14 +1107,14 @@ class DisplayMappingResults(object): elif (geneStartPix < xLeftOffset): geneStartPix = xLeftOffset; # clip the first in-range gene - outlineColor = pid.darkblue - fillColor = pid.darkblue + outlineColor = DARKBLUE + fillColor = DARKBLUE TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % (geneSymbol, float(txStart), float(txEnd), strand) # NL: 06-02-2011 Rob required to change this link for gene related HREF=geneNCBILink %geneSymbol else: - outlineColor = pid.orange - fillColor = pid.orange + outlineColor = ORANGE + fillColor = ORANGE TITLE = "Gene: %s" % geneSymbol #Draw Genes @@ -1287,7 +1308,7 @@ class DisplayMappingResults(object): drawit = 1 if drawit == 1: - myColor = pid.darkblue + myColor = DARKBLUE outlineColor = myColor fillColor = myColor @@ -1335,8 +1356,8 @@ class DisplayMappingResults(object): canvas.drawLine(drawStart, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2)) - fillColor=pid.black - outlineColor=pid.black + fillColor=BLACK + outlineColor=BLACK if lastGene == 0: canvas.drawRect(geneStartPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT*zoom, geneEndPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT+ 2*self.EACH_GENE_HEIGHT*zoom, edgeColor = outlineColor, fillColor = fillColor) @@ -1355,7 +1376,7 @@ class DisplayMappingResults(object): if lastGene == 0: - canvas.drawString("%s" % (_chr[j].name), geneStartPix , geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black, angle=-90) + canvas.drawString("%s" % (_chr[j].name), geneStartPix , geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=BLACK, angle=-90) oldgeneEndPix = geneEndPix; oldgeno = _chr[j].genotype @@ -1384,8 +1405,8 @@ class DisplayMappingResults(object): expr = item.value # Place where font is hardcoded - canvas.drawString("%s" % (samplelist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black) - canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black) + canvas.drawString("%s" % (samplelist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=BLACK) + canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=BLACK) ## END HaplotypeAnalyst @@ -1487,14 +1508,14 @@ class DisplayMappingResults(object): chrFont = pid.Font(ttf="verdana", size=26*zoom, bold=1) traitFont = pid.Font(ttf="verdana", size=14, bold=0) chrX = xLeftOffset + plotWidth - 2 - canvas.stringWidth("Chr %s" % self.ChrList[self.selectedChr][0], font=chrFont) - canvas.drawString("Chr %s" % self.ChrList[self.selectedChr][0], chrX, ensemblPaddingTop-5, font=chrFont, color=pid.gray) + canvas.drawString("Chr %s" % self.ChrList[self.selectedChr][0], chrX, ensemblPaddingTop-5, font=chrFont, color=GRAY) # end of drawBrowserClickableRegions else: #draw the gray text chrFont = pid.Font(ttf="verdana", size=26*zoom, bold=1) traitFont = pid.Font(ttf="verdana", size=14, bold=0) chrX = xLeftOffset + (plotWidth - canvas.stringWidth("Chr %s" % currentChromosome, font=chrFont))/2 - canvas.drawString("Chr %s" % currentChromosome, chrX, 32, font=chrFont, color=pid.gray) + canvas.drawString("Chr %s" % currentChromosome, chrX, 32, font=chrFont, color=GRAY) # end of drawBrowserClickableRegions pass @@ -1517,8 +1538,8 @@ class DisplayMappingResults(object): MBLabelFont = pid.Font(ttf="verdana", size=15*zoom, bold=0) xMajorTickHeight = 10 * zoom # How high the tick extends below the axis xMinorTickHeight = 5*zoom - xAxisTickMarkColor = pid.black - xAxisLabelColor = pid.black + xAxisTickMarkColor = BLACK + xAxisLabelColor = BLACK fontHeight = 12*fontZoom # How tall the font that we're using is spacingFromLabelToAxis = 5 @@ -1565,14 +1586,14 @@ class DisplayMappingResults(object): else: distScale = 5 for j, tickdists in enumerate(range(distScale, int(ceil(distLen)), distScale)): - canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=pid.black, width=1*zoom) + canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=BLACK, width=1*zoom) if j % 2 == 0: - canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=pid.black, font=MBLabelFont, angle=270) + canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=BLACK, font=MBLabelFont, angle=270) startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale megabaseLabelFont = pid.Font(ttf="verdana", size=18*zoom*1.5, bold=0) canvas.drawString("Megabases", xLeftOffset + (plotWidth - canvas.stringWidth("Megabases", font=megabaseLabelFont))/2, - strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=megabaseLabelFont, color=pid.black) + strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=megabaseLabelFont, color=BLACK) pass else: strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont) + 8 @@ -1619,7 +1640,7 @@ class DisplayMappingResults(object): LRectWidth = 10 LRectHeight = 3 offsetA = -stepA - lineColor = pid.lightblue + lineColor = LIGHTBLUE startPosX = xLeftOffset for j, ChrInfo in enumerate(ChrAInfo): @@ -1642,11 +1663,11 @@ class DisplayMappingResults(object): yZero+25, color=lineColor) canvas.drawLine(xLeftOffset+offsetA,yZero+25,xLeftOffset+offsetA,\ yZero+40+Zorder*(LRectWidth+3),color=lineColor) - rectColor = pid.orange + rectColor = ORANGE else: canvas.drawLine(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3,\ xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),color=lineColor) - rectColor = pid.deeppink + rectColor = DEEPPINK canvas.drawRect(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),\ xLeftOffset+offsetA-LRectHeight,yZero+40+Zorder*(LRectWidth+3)+LRectWidth,\ edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0) @@ -1663,9 +1684,9 @@ class DisplayMappingResults(object): centimorganLabelFont = pid.Font(ttf="verdana", size=18*zoom*1.5, bold=0) canvas.drawString("Centimorgans", xLeftOffset + (plotWidth - canvas.stringWidth("Megabases", font=centimorganLabelFont))/2, - strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=centimorganLabelFont, color=pid.black) + strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=centimorganLabelFont, color=BLACK) - canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=pid.black, width=X_AXIS_THICKNESS) # Draw the X axis itself + canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): @@ -1774,7 +1795,7 @@ class DisplayMappingResults(object): #draw the "LRS" or "LOD" string to the left of the axis canvas.drawString(self.LRS_LOD, xLeftOffset - max_lrs_width - 15*(zoom-1), \ - yZero - 150 - 300*(zoom - 1), font=LRSLODFont, color=pid.black, angle=90) + yZero - 150 - 300*(zoom - 1), font=LRSLODFont, color=BLACK, angle=90) for item in LRSAxisList: if LRS_LOD_Max == 0.0: @@ -1955,9 +1976,9 @@ class DisplayMappingResults(object): if self.manhattan_plot == True: if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1): - point_color = pid.red + point_color = RED else: - point_color = pid.blue + point_color = BLUE final_x_pos = Xc-canvas.stringWidth("5",font=symbolFont)/2+1 if final_x_pos > (xLeftOffset + plotWidth): @@ -2121,13 +2142,13 @@ class DisplayMappingResults(object): #draw the shaded boxes and the sig/sug thick lines canvas.drawRect(startPosX, yTopOffset, startPosX + self.ChrLengthDistList[i]*plotXScale, \ - yBottom, edgeColor=pid.gainsboro,fillColor=theBackColor) + yBottom, edgeColor=GAINSBORO,fillColor=theBackColor) chrNameWidth = canvas.stringWidth(_chr.name, font=chrLabelFont) chrStartPix = startPosX + (self.ChrLengthDistList[i]*plotXScale -chrNameWidth)/2 chrEndPix = startPosX + (self.ChrLengthDistList[i]*plotXScale +chrNameWidth)/2 - canvas.drawString(_chr.name, chrStartPix, yTopOffset + 20 ,font = chrLabelFont,color=pid.black) + canvas.drawString(_chr.name, chrStartPix, yTopOffset + 20 ,font = chrLabelFont,color=BLACK) COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20) #add by NL 09-03-2010 @@ -2379,4 +2400,4 @@ class DisplayMappingResults(object): lCorr = lCorr[0] break except: raise #lCorr = None - return lCorr
\ No newline at end of file + return lCorr |