diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 194 |
1 files changed, 170 insertions, 24 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 2ca1fa5f..44067a5d 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -429,6 +429,10 @@ class DisplayMappingResults: self.SNPChecked = start_vars['showSNP'] else: self.SNPChecked = False + if 'showHomology' in list(start_vars.keys()): + self.homologyChecked = start_vars['showHomology'] + else: + self.homologyChecked = False if 'showGenes' in list(start_vars.keys()): self.geneChecked = start_vars['showGenes'] else: @@ -490,28 +494,6 @@ class DisplayMappingResults: else: self.GraphInterval = self.cMGraphInterval # cM -# BEGIN HaplotypeAnalyst -# count the amount of individuals to be plotted, and increase self.graphHeight - if self.haplotypeAnalystChecked and self.selectedChr > -1: - thisTrait = self.this_trait - smd = [] - for sample in self.sample_vals_dict.keys(): - if self.sample_vals_dict[sample] != "x": - temp = GeneralObject(name=sample, value=float( - self.sample_vals_dict[sample])) - smd.append(temp) - else: - continue - samplelist = list(self.genotype.prgy) - for j, _geno in enumerate(self.genotype[0][1].genotype): - for item in smd: - if item.name == samplelist[j]: - self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1 -# default: - self.graphHeight = self.graphHeight + 2 * \ - (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT -# END HaplotypeAnalyst - ######################### # Get the sorting column ######################### @@ -550,7 +532,8 @@ class DisplayMappingResults: geneTable = "" self.geneCol = None - if self.plotScale == 'physic' and self.selectedChr > -1 and (self.intervalAnalystChecked or self.geneChecked): + self.homology = None + if self.plotScale == 'physic' and self.selectedChr > -1 and (self.intervalAnalystChecked or self.geneChecked or self.homologyChecked): # Draw the genes for this chromosome / region of this chromosome webqtldatabase = self.dataset.name @@ -561,6 +544,7 @@ class DisplayMappingResults: chrName = self.selectedChr self.geneCol = GeneUtil.loadGenes( str(chrName), self.diffCol, self.startMb, self.endMb, "mouse") + self.homology = GeneUtil.load_homology(str(chrName), self.startMb, self.endMb) elif self.dataset.group.species == "rat": if self.selectedChr == 21: chrName = "X" @@ -580,6 +564,34 @@ class DisplayMappingResults: self.geneTable(self.geneCol, GENEID) +# BEGIN HaplotypeAnalyst +# count the amount of individuals to be plotted, and increase self.graphHeight + if self.haplotypeAnalystChecked and self.selectedChr > -1: + thisTrait = self.this_trait + smd = [] + for sample in self.sample_vals_dict.keys(): + if self.sample_vals_dict[sample] != "x": + temp = GeneralObject(name=sample, value=float( + self.sample_vals_dict[sample])) + smd.append(temp) + else: + continue + samplelist = list(self.genotype.prgy) + for j, _geno in enumerate(self.genotype[0][1].genotype): + for item in smd: + if item.name == samplelist[j]: + self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1 +# default: + self.graphHeight = self.graphHeight + 2 * \ + (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT +# END HaplotypeAnalyst + + if self.homologyChecked and self.homology and (self.endMb - self.startMb < 2) and self.geneChecked and self.geneCol: + self.graphHeight = self.graphHeight + (self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT + if self.geneChecked and self.geneCol: + self.graphHeight = self.graphHeight + (self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT + + ################################################################ # Plots goes here ################################################################ @@ -685,9 +697,12 @@ class DisplayMappingResults: drawAreaHeight -= 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING + 10 * zoom else: drawAreaHeight -= 3 * self.BAND_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom + if self.homologyChecked: + drawAreaHeight -= self.NUM_GENE_ROWS * \ + self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING if self.geneChecked: drawAreaHeight -= self.NUM_GENE_ROWS * \ - self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom + self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING else: if self.selectedChr > -1: drawAreaHeight -= 20 @@ -720,9 +735,16 @@ class DisplayMappingResults: if self.plotScale == 'physic' and self.selectedChr > -1: self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + if self.geneChecked and self.geneCol: self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) + if self.homologyChecked and self.homology and (endMb - startMb < 2): + if self.geneChecked and self.geneCol: + yTopOffset = newoffset[3] + self.NUM_GENE_ROWS * \ + self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING + 10 + self.drawHomologyBand(canvas, gifmap, plotXScale, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), + zoom=zoom, startMb=startMb, endMb=endMb) if self.SNPChecked: self.drawSNPTrackNew( canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb=endMb) @@ -1317,6 +1339,130 @@ class DisplayMappingResults: text=string6, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) + def drawHomologyBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None): + im_drawer = ImageDraw.Draw(canvas) + if self.plotScale != 'physic' or self.selectedChr == -1 or not self.homology: + return + + xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset + plotWidth = canvas.size[0] - xLeftOffset - xRightOffset + plotHeight = canvas.size[1] - yTopOffset - yBottomOffset + yZero = canvas.size[1] - yBottomOffset + fontZoom = zoom + if zoom == 2: + fontZoom = 1.5 + + yPaddingTop = yTopOffset + + for index, homology_dict in enumerate(self.homology): + if self.dataset.group.species == "mouse": + mm10_start = homology_dict["mm10_start"] + mm10_end = homology_dict["mm10_end"] + hg38_chr = homology_dict["hg38_chr"] + hg38_strand = homology_dict["hg38_strand"] + hg38_start = homology_dict["hg38_start"] + hg38_end = homology_dict["hg38_end"] + geneLength = (mm10_end - mm10_start) * 1000.0 + tenPercentLength = geneLength * 0.0001 + + geneStartPix = xLeftOffset + \ + plotXScale * (float(mm10_start) - startMb) + geneEndPix = xLeftOffset + plotXScale * \ + (float(mm10_end) - startMb) # at least one pixel + + if (geneEndPix < xLeftOffset): + return # this gene is not on the screen + elif (geneEndPix > xLeftOffset + plotWidth): + geneEndPix = xLeftOffset + plotWidth # clip the last in-range gene + if (geneStartPix > xLeftOffset + plotWidth): + return # we are outside the valid on-screen range, so stop drawing genes + elif (geneStartPix < xLeftOffset): + geneStartPix = xLeftOffset # clip the first in-range gene + + # color the gene based on SNP density + # found earlier, needs to be recomputed as snps are added + # always apply colors now, even if SNP Track not checked - Zach 11/24/2010 + + myColor = BLACK + + outlineColor = myColor + fillColor = myColor + + TITLE = f"hg38: Chr {hg38_chr} from {hg38_start:.3f} to {hg38_end:.3f} Mb" + HREF = f"http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr{hg38_chr}:{int(hg38_start * 1000000)}-{int(hg38_end * 1000000)}" + + # Draw Genes + geneYLocation = yPaddingTop + \ + (index % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT * zoom + if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": + geneYLocation += 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING + else: + geneYLocation += 3 * self.BAND_HEIGHT + 3 * self.BAND_SPACING + + # draw the detail view + if self.endMb - self.startMb <= self.DRAW_DETAIL_MB and geneEndPix - geneStartPix > self.EACH_GENE_ARROW_SPACING * 3: + utrColor = ImageColor.getrgb("rgb(66%, 66%, 66%)") + arrowColor = ImageColor.getrgb("rgb(70%, 70%, 70%)") + + # draw the line that runs the entire length of the gene + im_drawer.line( + xy=( + (geneStartPix, geneYLocation + \ + self.EACH_GENE_HEIGHT / 2 * zoom), + (geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 * zoom)), + fill=outlineColor, width=1) + + # draw the arrows + if geneEndPix - geneStartPix < 1: + genePixRange = 1 + else: + genePixRange = int(geneEndPix - geneStartPix) + for xCoord in range(0, genePixRange): + + if (xCoord % self.EACH_GENE_ARROW_SPACING == 0 and xCoord + self.EACH_GENE_ARROW_SPACING < geneEndPix - geneStartPix) or xCoord == 0: + if hg38_strand == "+": + im_drawer.line( + xy=((geneStartPix + xCoord, geneYLocation), + (geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, + geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), + fill=arrowColor, width=1) + im_drawer.line( + xy=((geneStartPix + xCoord, + geneYLocation + self.EACH_GENE_HEIGHT * zoom), + (geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, + geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), + fill=arrowColor, width=1) + else: + im_drawer.line( + xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, + geneYLocation), + (geneStartPix + xCoord, + geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), + fill=arrowColor, width=1) + im_drawer.line( + xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, + geneYLocation + self.EACH_GENE_HEIGHT * zoom), + (geneStartPix + xCoord, + geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), + fill=arrowColor, width=1) + # draw the genes as rectangles + else: + im_drawer.rectangle( + xy=((geneStartPix, geneYLocation), + (geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT * zoom))), + outline=outlineColor, fill=fillColor) + + COORDS = "%d, %d, %d, %d" % ( + geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) + # NL: 06-02-2011 Rob required to display NCBI info in a new window + gifmap.append( + HtmlGenWrapper.create_area_tag( + shape='rect', + coords=COORDS, + href=HREF, + title=TITLE, + target="_blank")) + def drawGeneBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None): im_drawer = ImageDraw.Draw(canvas) if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol: |