# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it # under the terms of the GNU Affero General Public License # as published by the Free Software Foundation, either version 3 of the # License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # See the GNU Affero General Public License for more details. # # This program is available from Source Forge: at GeneNetwork Project # (sourceforge.net/projects/genenetwork/). # # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) # at rwilliams@uthsc.edu and xzhou15@uthsc.edu # # # # This module is used by GeneNetwork project (www.genenetwork.org) # # Created by GeneNetwork Core Team 2010/08/10 # # Last updated by Zach 12/14/2010 import datetime import string from math import * from PIL import Image from PIL import ImageDraw from PIL import ImageFont from PIL import ImageColor import os import json import htmlgen as HT from gn2.base import webqtlConfig from gn2.base.GeneralObject import GeneralObject from gn2.utility import webqtlUtil from gn2.utility import Plot from gn2.utility.tools import get_setting from gn2.wqflask.interval_analyst import GeneUtil from gn2.base.webqtlConfig import GENERATED_IMAGE_DIR from gn2.utility.pillow_utils import draw_rotated_text, draw_open_polygon from gn2.wqflask.database import database_connection try: # Only import this for Python3 from functools import reduce except: pass 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 ---- # # ZS: List of distinct colors for manhattan plot if user selects "varied" COLOR_CODES = ["#FF0000", "#00FF00", "#0000FF", "#FFFF00", "#FF00FF", "#00FFFF", "#000000", "#800000", "#008000", "#000080", "#808000", "#800080", "#008080", "#808080", "#C00000", "#00C000", "#0000C0", "#C0C000", "#C000C0", "#00C0C0", "#C0C0C0", "#400000", "#004000", "#000040"] DISTINCT_COLOR_LIST = [ImageColor.getrgb(color) for color in COLOR_CODES] # ---- FONT FILES ---- # VERDANA_FILE = "./gn2/wqflask/static/fonts/verdana.ttf" VERDANA_BOLD_FILE = "./gn2/wqflask/static/fonts/verdanab.ttf" TREBUC_FILE = "./gn2/wqflask/static/fonts/trebucbd.ttf" FNT_BS_FILE = "./gn2/wqflask/static/fonts/fnt_bs.ttf" ARIAL_FILE = "./gn2/wqflask/static/fonts/arial.ttf" assert(os.path.isfile(VERDANA_FILE)) class HtmlGenWrapper: """Wrapper Methods for HTML gen""" @staticmethod def create_image_tag(**kwargs): image = HT.Image("", "") for key, value in list(kwargs.items()): image.set_attribute(key, value) return image @staticmethod def create_form_tag(**kwargs): form = HT.Form("POST", "") # Default method is POST for key, value in list(kwargs.items()): if key == "submit": form.append(value) continue form.set_attribute(key.replace("cgi", "action"), str(value)) return form @staticmethod def create_p_tag(**kwargs): paragraph = HT.Paragraph() for key, value in list(kwargs.items()): paragraph.set_attribute(key, value) return paragraph @staticmethod def create_br_tag(): return HT.VoidElement("br") @staticmethod def create_input_tag(**kwargs): input_ = HT.Input() for key, value in list(kwargs.items()): input_.set_attribute(key.lower().replace("_", ""), value) return input_ @staticmethod def create_area_tag(**kwargs): area = HT.VoidElement("area") for key, value in list(kwargs.items()): area.set_attribute(key, value) return area @staticmethod def create_link_tag(href, content, **kwargs): link = HT.Link(href, content) for key, value in list(kwargs.items()): link.set_attribute(key, value) return link @staticmethod def create_map_tag(**kwargs): map_ = HT.Element("map") for key, value in list(kwargs.items()): map_.set_attribute(key, value) return map_ class DisplayMappingResults: """Inteval Mapping Plot Page""" cMGraphInterval = 5 GRAPH_MIN_WIDTH = 900 GRAPH_MAX_WIDTH = 10000 # Don't set this too high GRAPH_DEFAULT_WIDTH = 1280 MULT_GRAPH_DEFAULT_WIDTH = 2000 MULT_GRAPH_MIN_WIDTH = 1400 MULT_GRAPH_DEFAULT_WIDTH = 1600 GRAPH_DEFAULT_HEIGHT = 600 # Display order: # UCSC BAND ========= # ENSEMBL BAND -=-=-= # ** GENES ********** BAND_SPACING = 4 BAND_HEIGHT = 10 BAND_HEIGHT = 10 BAND_HEIGHT = 10 NUM_GENE_ROWS = 10 EACH_GENE_HEIGHT = 6 # number of pixels tall, for each gene to display EACH_GENE_ARROW_WIDTH = 5 EACH_GENE_ARROW_SPACING = 14 DRAW_DETAIL_MB = 4 DRAW_UTR_LABELS_MB = 4 qmarkImg = HtmlGenWrapper.create_image_tag( src='/images/qmarkBoxBlue.gif', width="10", height="13", border="0", alt='Glossary' ) # Note that "qmark.gif" is a similar, smaller, rounded-edges # question mark. It doesn't look like the ones on the image, # though, which is why we don't use it here. HELP_WINDOW_NAME = 'helpWind' # BEGIN HaplotypeAnalyst NR_INDIVIDUALS = 0 # END HaplotypeAnalyst ALEX_DEBUG_BOOL_PRINT_GENE_LIST = 1 kONE_MILLION = 1000000 LODFACTOR = 4.61 SNP_COLOR = ORANGE # Color for the SNP "seismograph" TRANSCRIPT_LOCATION_COLOR = MEDIUMPURPLE 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 = GREEN ADDITIVE_COLOR_NEGATIVE = ORANGE DOMINANCE_COLOR_POSITIVE = DARKVIOLET DOMINANCE_COLOR_NEGATIVE = RED # BEGIN HaplotypeAnalyst HAPLOTYPE_POSITIVE = GREEN HAPLOTYPE_NEGATIVE = RED HAPLOTYPE_HETEROZYGOUS = BLUE HAPLOTYPE_RECOMBINATION = DARKGRAY # END HaplotypeAnalyst TOP_RIGHT_INFO_COLOR = BLACK 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 = ImageColor.getrgb("#A2FB94") CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR = ImageColor.getrgb("#CEFEC7") CLICKABLE_PHENOGEN_TEXT_COLOR = ImageColor.getrgb("#1FD504") 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 = ImageColor.getrgb("#EEEEDD") CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR = ImageColor.getrgb("#FEFEEE") CLICKABLE_ENSEMBL_TEXT_COLOR = ImageColor.getrgb("#555500") GRAPH_BACK_LIGHT_COLOR = ImageColor.getrgb("#FBFBFF") GRAPH_BACK_DARK_COLOR = ImageColor.getrgb("#F1F1F9") HELP_PAGE_REF = '/glossary.html' def __init__(self, start_vars): self.temp_uuid = start_vars['temp_uuid'] self.hash_of_inputs = start_vars['hash_of_inputs'] self.dataid = start_vars['dataid'] self.dataset = start_vars['dataset'] self.this_trait = start_vars['this_trait'] self.n_samples = start_vars['n_samples'] self.species = start_vars['species'] self.genofile_string = "" if 'genofile_string' in start_vars: self.genofile_string = start_vars['genofile_string'] self.geno_db_exists = start_vars['geno_db_exists'] self.first_run = True if 'first_run' in start_vars: self.first_run = start_vars['first_run'] if 'temp_trait' in start_vars and start_vars['temp_trait'] != "False": self.temp_trait = "True" self.group = start_vars['group'] # Needing for form submission when doing single chr # mapping or remapping after changing options self.sample_vals = start_vars['sample_vals'] self.vals_hash= start_vars['vals_hash'] self.sample_vals_dict = json.loads(self.sample_vals) self.transform = start_vars['transform'] self.mapping_method = start_vars['mapping_method'] self.mapping_results_path = start_vars['mapping_results_path'] if self.mapping_method == "rqtl_geno": self.mapmethod_rqtl = start_vars['method'] self.mapmodel_rqtl = start_vars['model'] self.pair_scan = start_vars['pair_scan'] self.js_data = start_vars['js_data'] # Top markers to display in table self.trimmed_markers = start_vars['trimmed_markers'] if self.dataset.group.species == "rat": self._ucscDb = "rn6" elif self.dataset.group.species == "mouse": self._ucscDb = "mm10" else: self._ucscDb = "" ##################################### # Options ##################################### # Mapping options if start_vars['mapping_scale'] != "": self.plotScale = start_vars['mapping_scale'] else: self.plotScale = "physic" self.manhattan_plot = start_vars['manhattan_plot'] if self.manhattan_plot: self.color_scheme = "alternating" if 'color_scheme' in start_vars: self.color_scheme = start_vars['color_scheme'] if self.color_scheme == "single": self.manhattan_single_color = ImageColor.getrgb( "#" + start_vars['manhattan_single_color']) if 'permCheck' in list(start_vars.keys()): self.permChecked = start_vars['permCheck'] else: self.permChecked = False if start_vars['num_perm'] > 0: self.nperm = int(start_vars['num_perm']) if self.permChecked: self.perm_output = start_vars['perm_output'] self.suggestive = start_vars['suggestive'] self.significant = start_vars['significant'] else: self.nperm = 0 if 'bootCheck' in list(start_vars.keys()): self.bootChecked = start_vars['bootCheck'] else: self.bootChecked = False if 'num_bootstrap' in list(start_vars.keys()): self.nboot = int(start_vars['num_bootstrap']) else: self.nboot = 0 if 'bootstrap_results' in list(start_vars.keys()): self.bootResult = start_vars['bootstrap_results'] else: self.bootResult = [] if 'do_control' in list(start_vars.keys()): self.doControl = start_vars['do_control'] else: self.doControl = "false" if 'control_marker' in list(start_vars.keys()): self.controlLocus = start_vars['control_marker'] else: self.controlLocus = "" if 'covariates' in list(start_vars.keys()): self.covariates = start_vars['covariates'] if 'maf' in list(start_vars.keys()): self.maf = start_vars['maf'] else: self.maf = "" if 'output_files' in list(start_vars.keys()): self.output_files = start_vars['output_files'] if 'use_loco' in list(start_vars.keys()) and self.mapping_method == "gemma": self.use_loco = start_vars['use_loco'] if self.mapping_method == "reaper": if 'output_files' in start_vars: self.output_files = ",".join( [(the_file if the_file is not None else "") for the_file in start_vars['output_files']]) self.categorical_vars = "" self.perm_strata = "" if 'perm_strata' in list(start_vars.keys()) and 'categorical_vars' in list(start_vars.keys()): self.categorical_vars = start_vars['categorical_vars'] self.perm_strata = start_vars['perm_strata'] self.selectedChr = int(start_vars['selected_chr']) self.strainlist = start_vars['samples'] self.traitList = [] thisTrait = start_vars['this_trait'] self.traitList.append(thisTrait) ################################################################ # Calculations QTL goes here ################################################################ self.multipleInterval = len(self.traitList) > 1 self.qtlresults = start_vars['qtl_results'] if self.multipleInterval: self.colorCollection = Plot.colorSpectrum(len(self.qtlresults)) else: self.colorCollection = [self.LRS_COLOR] self.dataset.group.genofile = self.genofile_string.split(":")[0] if self.mapping_method == "reaper" and self.manhattan_plot != True: self.genotype = self.dataset.group.read_genotype_file( use_reaper=True) else: self.genotype = self.dataset.group.read_genotype_file() # Drawing Options try: if self.selectedChr > -1: self.graphWidth = min(self.GRAPH_MAX_WIDTH, max( self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) else: self.graphWidth = min(self.GRAPH_MAX_WIDTH, max( self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth']))) except: if self.selectedChr > -1: self.graphWidth = self.GRAPH_DEFAULT_WIDTH else: self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH # BEGIN HaplotypeAnalyst if 'haplotypeAnalystCheck' in list(start_vars.keys()): self.haplotypeAnalystChecked = start_vars['haplotypeAnalystCheck'] else: self.haplotypeAnalystChecked = False # END HaplotypeAnalyst self.graphHeight = self.GRAPH_DEFAULT_HEIGHT self.dominanceChecked = False if 'LRSCheck' in list(start_vars.keys()): self.LRS_LOD = start_vars['LRSCheck'] else: self.LRS_LOD = start_vars['score_type'] self.intervalAnalystChecked = True self.draw2X = False if 'additiveCheck' in list(start_vars.keys()): self.additiveChecked = start_vars['additiveCheck'] else: self.additiveChecked = False if 'viewLegend' in list(start_vars.keys()): self.legendChecked = start_vars['viewLegend'] else: self.legendChecked = False if 'showSNP' in list(start_vars.keys()): self.SNPChecked = start_vars['showSNP'] else: self.SNPChecked = False if 'showHomology' in list(start_vars.keys()): self.homologyChecked = start_vars['showHomology'] else: self.homologyChecked = "ON" if 'showGenes' in list(start_vars.keys()): self.geneChecked = start_vars['showGenes'] else: self.geneChecked = False try: self.startMb = float(start_vars['startMb']) except: self.startMb = -1 try: self.endMb = float(start_vars['endMb']) except: self.endMb = -1 try: self.lrsMax = float(start_vars['lrsMax']) except: self.lrsMax = 0 # Trait Infos self.identification = "" ################################################################ # Generate Chr list and Retrieve Length Information ################################################################ self.ChrList = [("All", -1)] for i, indChr in enumerate(self.genotype): if self.dataset.group.species == "mouse" and indChr.name == "20": self.ChrList.append(("X", i)) elif self.dataset.group.species == "rat" and indChr.name == "21": self.ChrList.append(("X", i)) self.ChrList.append((indChr.name, i)) with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: cursor.execute("SELECT Length FROM Chr_Length, InbredSet " "WHERE Chr_Length.SpeciesId = InbredSet.SpeciesId " "AND InbredSet.Name = %s AND Chr_Length.Name IN " f"({', '.join(['%s' for x in self.ChrList[1:]])}) " "ORDER BY Chr_Length.OrderId", (self.dataset.group.name, *[x[0] for x in self.ChrList[1:]],)) self.ChrLengthMbList = cursor.fetchall() self.ChrLengthMbList = [x[0] / 1000000.0 for x in self.ChrLengthMbList] self.ChrLengthMbSum = reduce( lambda x, y: x + y, self.ChrLengthMbList, 0.0) if self.ChrLengthMbList: self.MbGraphInterval = self.ChrLengthMbSum / \ (len(self.ChrLengthMbList) * 12) # Empirical Mb interval else: self.MbGraphInterval = 1 self.ChrLengthCMList = [] for i, _chr in enumerate(self.genotype): self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM) self.ChrLengthCMSum = reduce( lambda x, y: x + y, self.ChrLengthCMList, 0.0) if self.plotScale == 'physic': self.GraphInterval = self.MbGraphInterval # Mb else: self.GraphInterval = self.cMGraphInterval # cM ######################### # Get the sorting column ######################### RISet = self.dataset.group.name if RISet in ('AXB', 'BXA', 'AXBXA'): self.diffCol = ['B6J', 'A/J'] elif RISet in ('BXD', 'BXD300', 'B6D2F2', 'BDF2-2005', 'BDF2-1999', 'BHHBF2', 'BXD-Harvested', 'BXD-Longevity', 'BXD-Micturition', 'BXD-AE', 'BXD-NIA-AD', 'B6D2RI', 'BXD-Bone', 'DOD-BXD-GWI', 'BXD-Heart-Metals', 'UTHSC-Cannabinoid'): self.diffCol = ['B6J', 'D2J'] elif RISet in ('CXB'): self.diffCol = ['CBY', 'B6J'] elif RISet in ('BXH', 'BHF2'): self.diffCol = ['B6J', 'C3H'] elif RISet in ('B6BTBRF2'): self.diffCol = ['B6J', 'BTB'] elif RISet in ('LXS'): self.diffCol = ['ILS', 'ISS'] else: self.diffCol = [] for i, strain in enumerate(self.diffCol): with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: cursor.execute("SELECT Id FROM Strain WHERE Symbol = %s", (strain,)) if result := cursor.fetchone(): self.diffCol[i] = result[0] ################################################################ # GeneCollection goes here ################################################################ if self.plotScale == 'physic' and self.selectedChr != -1: #StartMb or EndMb if self.startMb < 0 or self.endMb < 0: self.startMb = 0 self.endMb = self.ChrLengthMbList[self.selectedChr - 1] geneTable = "" self.geneCol = None 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 if self.dataset.group.species == "mouse": if self.selectedChr == 20: chrName = "X" else: 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, "mouse_to_human.csv") elif self.dataset.group.species == "rat": if self.selectedChr == 21: chrName = "X" else: chrName = self.selectedChr self.geneCol = GeneUtil.loadGenes( str(chrName), self.diffCol, self.startMb, self.endMb, "rat") if self.geneCol and self.intervalAnalystChecked: ####################################################################### #Nick use GENEID as RefGene to get Literature Correlation Informations# #For Interval Mapping, Literature Correlation isn't useful, so skip it# #through set GENEID is None # ####################################################################### GENEID = None 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.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 ################################################################ showLocusForm = "" intCanvas = Image.new("RGBA", size=(self.graphWidth, self.graphHeight)) gifmap = self.plotIntMapping( intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm=showLocusForm) self.gifmap = gifmap.__str__() self.filename = webqtlUtil.genRandStr("Itvl_") intCanvas.save( "{}.png".format( os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename)), format='png') intImg = HtmlGenWrapper.create_image_tag( src="/image/{}.png".format(self.filename), border="0", usemap='#WebQTLImageMap' ) # Scales plot differently for high resolution if self.draw2X: intCanvasX2 = Image.new("RGBA", size=( self.graphWidth * 2, self.graphHeight * 2)) gifmapX2 = self.plotIntMapping( intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm=showLocusForm, zoom=2) intCanvasX2.save( "{}.png".format( os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename + "X2")), format='png') ################################################################ # Outputs goes here ################################################################ # this form is used for opening Locus page or trait page, only available for genetic mapping if showLocusForm: showLocusForm = HtmlGenWrapper.create_form_tag( cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=showLocusForm, submit=HtmlGenWrapper.create_input_tag(type_='hidden')) hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet + \ "Geno", 'CellID': '_', 'RISet': fd.RISet, 'incparentsf1': 'ON'} for key in hddn.keys(): showLocusForm.append(HtmlGenWrapper.create_input_tag( name=key, value=hddn[key], type_='hidden')) showLocusForm.append(intImg) else: showLocusForm = intImg if (self.permChecked and self.nperm > 0) and not (self.multipleInterval and 0 < self.nperm): self.perm_filename = self.drawPermutationHistogram() ################################################################ # footnote goes here ################################################################ # Small('More information about this graph is available here.') btminfo = HtmlGenWrapper.create_p_tag(id="smallsize") if self.traitList and self.traitList[0].dataset and self.traitList[0].dataset.type == 'Geno': btminfo.append(HtmlGenWrapper.create_br_tag()) btminfo.append( 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.') def plotIntMapping(self, canvas, offset=(80, 120, 110, 100), zoom=1, startMb=None, endMb=None, showLocusForm=""): im_drawer = ImageDraw.Draw(canvas) # calculating margins xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset if self.multipleInterval: yTopOffset = max(90, yTopOffset) else: if self.legendChecked: yTopOffset += 10 if self.covariates != "" and self.controlLocus and self.doControl != "false": yTopOffset += 25 if len(self.transform) > 0: yTopOffset += 5 else: pass if self.plotScale != 'physic': yBottomOffset = max(120, yBottomOffset) fontZoom = zoom if zoom == 2: xLeftOffset += 20 fontZoom = 1.5 xLeftOffset = int(xLeftOffset * fontZoom) xRightOffset = int(xRightOffset * fontZoom) yBottomOffset = int(yBottomOffset * fontZoom) cWidth = canvas.size[0] cHeight = canvas.size[1] plotWidth = cWidth - xLeftOffset - xRightOffset plotHeight = cHeight - yTopOffset - yBottomOffset # Drawing Area Height drawAreaHeight = plotHeight if self.plotScale == 'physic' and self.selectedChr > -1: if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": 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 else: if self.selectedChr > -1: drawAreaHeight -= 20 else: drawAreaHeight -= 30 # BEGIN HaplotypeAnalyst if self.haplotypeAnalystChecked and self.selectedChr > -1: drawAreaHeight -= self.EACH_GENE_HEIGHT * \ (self.NR_INDIVIDUALS + 10) * 2 * zoom # END HaplotypeAnalyst if zoom == 2: drawAreaHeight -= 60 # Image map gifmap = HtmlGenWrapper.create_map_tag(name="WebQTLImageMap") newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset) # Draw the alternating-color background first and get plotXScale 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) # Draw clickable region and gene band if selected 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: 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) # BEGIN HaplotypeAnalyst if self.haplotypeAnalystChecked: self.drawHaplotypeBand( canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # END HaplotypeAnalyst # Draw X axis self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # Draw QTL curve self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb) # draw legend if self.multipleInterval: self.drawMultiTraitName( fd, canvas, gifmap, showLocusForm, offset=newoffset) elif self.legendChecked: self.drawLegendPanel(canvas, offset=newoffset, zoom=zoom) else: pass # draw position, no need to use a separate function self.drawProbeSetPosition( canvas, plotXScale, offset=newoffset, zoom=zoom) return gifmap def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None): im_drawer = ImageDraw.Draw(canvas) 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 bootHeightThresh = drawAreaHeight * 3 / 4 # break bootstrap result into groups BootCoord = [] i = 0 previous_chr = None previous_chr_as_int = 0 startX = xLeftOffset BootChrCoord = [] if self.selectedChr == -1: # ZS: If viewing full genome/all chromosomes for i, result in enumerate(self.qtlresults): if result['chr'] != previous_chr: previous_chr = result['chr'] previous_chr_as_int += 1 if previous_chr_as_int != 1: BootCoord.append(BootChrCoord) BootChrCoord = [] startX += ( self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval) * plotXScale if self.plotScale == 'physic': Xc = startX + (result['Mb'] - self.startMb) * plotXScale else: Xc = startX + \ (result['cM'] - self.qtlresults[0]['cM']) * plotXScale BootChrCoord.append([Xc, self.bootResult[i]]) else: for i, result in enumerate(self.qtlresults): if str(result['chr']) == str(self.ChrList[self.selectedChr][0]): if self.plotScale == 'physic': Xc = startX + (result['Mb'] - \ self.startMb) * plotXScale else: Xc = startX + \ (result['cM'] - self.qtlresults[0] ['cM']) * plotXScale BootChrCoord.append([Xc, self.bootResult[i]]) BootCoord = [BootChrCoord] # reduce bootResult if self.selectedChr > -1: maxBootBar = 80.0 else: maxBootBar = 200.0 stepBootStrap = plotWidth / maxBootBar reducedBootCoord = [] maxBootCount = 0 for BootChrCoord in BootCoord: nBoot = len(BootChrCoord) bootStartPixX = BootChrCoord[0][0] bootCount = BootChrCoord[0][1] for i in range(1, nBoot): if BootChrCoord[i][0] - bootStartPixX < stepBootStrap: bootCount += BootChrCoord[i][1] continue else: if maxBootCount < bootCount: maxBootCount = bootCount # end if reducedBootCoord.append( [bootStartPixX, BootChrCoord[i][0], bootCount]) bootStartPixX = BootChrCoord[i][0] bootCount = BootChrCoord[i][1] # end else # end for # add last piece if BootChrCoord[-1][0] - bootStartPixX > stepBootStrap / 2.0: reducedBootCoord.append( [bootStartPixX, BootChrCoord[-1][0], bootCount]) else: reducedBootCoord[-1][2] += bootCount reducedBootCoord[-1][1] = BootChrCoord[-1][0] # end else if maxBootCount < reducedBootCoord[-1][2]: maxBootCount = reducedBootCoord[-1][2] # end if for item in reducedBootCoord: if item[2] > 0: if item[0] < xLeftOffset: item[0] = xLeftOffset if item[0] > xLeftOffset + plotWidth: item[0] = xLeftOffset + plotWidth if item[1] < xLeftOffset: item[1] = xLeftOffset if item[1] > xLeftOffset + plotWidth: item[1] = xLeftOffset + plotWidth if item[0] != item[1]: im_drawer.rectangle( xy=((item[0], yZero), (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) bootScale = Plot.frange( bootScale[0], bootScale[1], bootScale[1] / bootScale[2]) bootScale = bootScale[:-1] + [highestPercent] bootOffset = 50 * fontZoom bootScaleFont = ImageFont.truetype( font=VERDANA_FILE, size=13 * fontZoom) im_drawer.rectangle( xy=((canvas.size[0] - bootOffset, yZero - bootHeightThresh), (canvas.size[0] - bootOffset - 15 * zoom, yZero)), fill=YELLOW, outline=BLACK) im_drawer.line( xy=((canvas.size[0] - bootOffset + 4, yZero), (canvas.size[0] - bootOffset, yZero)), fill=BLACK) TEXT_Y_DISPLACEMENT = -8 im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, yZero + TEXT_Y_DISPLACEMENT), text='0%', font=bootScaleFont, fill=BLACK) for item in bootScale: if item == 0: continue bootY = yZero - bootHeightThresh * item / highestPercent im_drawer.line( xy=((canvas.size[0] - bootOffset + 4, bootY), (canvas.size[0] - bootOffset, bootY)), fill=BLACK) im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, bootY + TEXT_Y_DISPLACEMENT), text='%2.1f' % item, font=bootScaleFont, fill=BLACK) if self.legendChecked: if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'): startPosY = 30 else: startPosY = 15 smallLabelFont = ImageFont.truetype( font=TREBUC_FILE, size=12 * fontZoom) leftOffset = canvas.size[0] - xRightOffset - 190 im_drawer.rectangle( xy=((leftOffset, startPosY - 6), (leftOffset + 12, startPosY + 6)), fill=YELLOW, outline=BLACK) im_drawer.text(xy=(canvas.size[0] - xRightOffset - 170, startPosY + TEXT_Y_DISPLACEMENT), text='Frequency of the Peak LRS', font=smallLabelFont, fill=BLACK) def drawProbeSetPosition(self, canvas, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None): im_drawer = ImageDraw.Draw(canvas) if len(self.traitList) != 1: 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 try: Chr = self.traitList[0].chr Mb = self.traitList[0].mb except: return previous_chr = 1 previous_chr_as_int = 0 if self.plotScale == "physic": this_chr = str(self.ChrList[self.selectedChr][0]) else: this_chr = str(self.ChrList[self.selectedChr][1] + 1) if self.plotScale == 'physic': if self.selectedChr > -1: if this_chr != Chr or Mb < self.startMb or Mb > self.endMb: return else: locPixel = xLeftOffset + (Mb - self.startMb) * plotXScale else: locPixel = xLeftOffset for i, _chr in enumerate(self.ChrList[1:]): if _chr[0] != Chr: locPixel += (self.ChrLengthDistList[i] + \ self.GraphInterval) * plotXScale else: locPixel += Mb * plotXScale break else: if self.selectedChr > -1: for i, qtlresult in enumerate(self.qtlresults): if qtlresult['chr'] != self.selectedChr: continue if i == 0 and qtlresult['Mb'] >= Mb: locPixel = -1 break # the trait's position is between two traits if i > 0 and self.qtlresults[i - 1]['Mb'] < Mb and qtlresult['Mb'] >= Mb: locPixel = xLeftOffset + plotXScale * (self.qtlresults[i - 1]['Mb'] + (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']) * ( Mb - self.qtlresults[i - 1]['Mb']) / (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb'])) break # the trait's position is on the right of the last genotype if i == len(self.qtlresults) and Mb >= qtlresult['Mb']: locPixel = -1 else: locPixel = xLeftOffset for i, _chr in enumerate(self.ChrList): if i < (len(self.ChrList) - 1): if _chr != Chr: locPixel += (self.ChrLengthDistList[i] + \ self.GraphInterval) * plotXScale else: locPixel += (Mb * (_chr[-1].cM - _chr[0].cM) / \ self.ChrLengthCMList[i]) * plotXScale break if locPixel >= 0 and self.plotScale == 'physic': traitPixel = ((locPixel, yZero), (locPixel - 7, yZero + 14), (locPixel + 7, yZero + 14)) draw_open_polygon(canvas, xy=traitPixel, outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR) def drawSNPTrackNew(self, canvas, 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.diffCol: return SNP_HEIGHT_MODIFIER = 18.0 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 drawSNPLocationY = yTopOffset + plotHeight #chrName = self.genotype[0].name chrName = self.ChrList[self.selectedChr][0] stepMb = (endMb - startMb) / plotWidth strainId1, strainId2 = self.diffCol SNPCounts = [] while startMb < endMb: with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: # snp count cursor.execute("SELECT COUNT(*) FROM BXDSnpPosition " "WHERE Chr = %s AND Mb >= %s AND Mb < %s AND " "StrainId1 = %s AND StrainId2 = %s", (chrName, f"{startMb:2.6f}", f"{startMb + stepMb:2.6f}", strainId1, strainId2,)) SNPCounts.append(cursor.fetchone()[0]) startMb += stepMb if (len(SNPCounts) > 0): maxCount = max(SNPCounts) if maxCount > 0: for i in range(xLeftOffset, xLeftOffset + plotWidth): snpDensity = float( SNPCounts[i - xLeftOffset] * SNP_HEIGHT_MODIFIER / maxCount) im_drawer.line( xy=((i, drawSNPLocationY + (snpDensity) * zoom), (i, drawSNPLocationY - (snpDensity) * zoom)), fill=self.SNP_COLOR, width=1) def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset=(40, 120, 80, 10), zoom=1): nameWidths = [] yPaddingTop = 10 colorFont = ImageFont.truetype(font=TREBUC_FILE, size=12) if len(self.qtlresults) > 20 and self.selectedChr > -1: rightShift = 20 rightShiftStep = 60 rectWidth = 10 else: rightShift = 40 rightShiftStep = 80 rectWidth = 15 for k, thisTrait in enumerate(self.traitList): thisLRSColor = self.colorCollection[k] kstep = k % 4 if k != 0 and kstep == 0: if nameWidths: rightShiftStep = max(nameWidths[-4:]) + rectWidth + 20 rightShift += rightShiftStep name = thisTrait.displayName() nameWidth, nameHeight = im_drawer.textsize(name, font=colorFont) nameWidths.append(nameWidth) im_drawer.rectangle( xy=((rightShift, yPaddingTop + kstep * 15), (rectWidth + rightShift, yPaddingTop + 10 + kstep * 15)), fill=thisLRSColor, outline=BLACK) im_drawer.text( text=name, xy=(rectWidth + 2 + rightShift, yPaddingTop + 10 + kstep * 15), font=colorFont, fill=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) Areas = HtmlGenWrapper.create_area_tag( shape='rect', coords=COORDS, href=HREF) gifmap.append(Areas) # TODO def drawLegendPanel(self, canvas, offset=(40, 120, 80, 10), zoom=1): im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset plotHeight = canvas.size[1] - yTopOffset - yBottomOffset yZero = canvas.size[1] - yBottomOffset TEXT_Y_DISPLACEMENT = -8 fontZoom = zoom if zoom == 2: fontZoom = 1.5 labelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom) startPosY = 15 stepPosY = 12 * fontZoom startPosX = canvas.size[0] - xRightOffset - 415 if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'): startPosY = 15 nCol = 2 smallLabelFont = ImageFont.truetype( font=TREBUC_FILE, size=12 * fontZoom) leftOffset = canvas.size[0] - xRightOffset - 190 draw_open_polygon( canvas, xy=( (leftOffset + 6, startPosY - 7), (leftOffset - 1, startPosY + 7), (leftOffset + 13, startPosY + 7)), outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR ) TEXT_Y_DISPLACEMENT = -8 im_drawer.text( text="Sequence Site", xy=(leftOffset + 20, startPosY + TEXT_Y_DISPLACEMENT), font=smallLabelFont, fill=self.TOP_RIGHT_INFO_COLOR) if self.manhattan_plot != True: im_drawer.line( xy=((startPosX, startPosY), (startPosX + 32, startPosY)), fill=self.LRS_COLOR, width=2) im_drawer.text( text=self.LRS_LOD, xy=( startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) startPosY += stepPosY if self.additiveChecked: im_drawer.line( xy=((startPosX, startPosY), (startPosX + 17, startPosY)), fill=self.ADDITIVE_COLOR_POSITIVE, width=2) im_drawer.line( xy=((startPosX + 18, startPosY), (startPosX + 32, startPosY)), fill=self.ADDITIVE_COLOR_NEGATIVE, width=2) im_drawer.text( text='Additive Effect', xy=(startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) startPosY += stepPosY if self.genotype.type == 'intercross' and self.dominanceChecked: im_drawer.line( xy=((startPosX, startPosY), (startPosX + 17, startPosY)), fill=self.DOMINANCE_COLOR_POSITIVE, width=4) im_drawer.line( xy=((startPosX + 18, startPosY), (startPosX + 35, startPosY)), fill=self.DOMINANCE_COLOR_NEGATIVE, width=4) im_drawer.text( text='Dominance Effect', xy=(startPosX + 42, startPosY + 5), font=labelFont, fill=BLACK) startPosY += stepPosY if self.haplotypeAnalystChecked: im_drawer.line( xy=((startPosX - 34, startPosY), (startPosX - 17, startPosY)), fill=self.HAPLOTYPE_POSITIVE, width=4) im_drawer.line( xy=((startPosX - 17, startPosY), (startPosX, startPosY)), fill=self.HAPLOTYPE_NEGATIVE, width=4) im_drawer.line( xy=((startPosX, startPosY), (startPosX + 17, startPosY)), fill=self.HAPLOTYPE_HETEROZYGOUS, width=4) im_drawer.line( xy=((startPosX + 17, startPosY), (startPosX + 34, startPosY)), fill=self.HAPLOTYPE_RECOMBINATION, width=4) im_drawer.text( text='Haplotypes (Pat, Mat, Het, Unk)', xy=(startPosX + 41, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) startPosY += stepPosY if self.permChecked and self.nperm > 0: thisStartX = startPosX if self.multipleInterval and not self.bootChecked: thisStartX = canvas.size[0] - xRightOffset - 205 im_drawer.line( xy=((thisStartX, startPosY), (startPosX + 32, startPosY)), fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH) im_drawer.line( xy=((thisStartX, startPosY + stepPosY), (startPosX + 32, startPosY + stepPosY)), fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH) im_drawer.text( text='Significant %s = %2.2f' % ( self.LRS_LOD, self.significant), xy=(thisStartX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) im_drawer.text( text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive), xy=(thisStartX + 40, startPosY + TEXT_Y_DISPLACEMENT + stepPosY), font=labelFont, fill=BLACK) labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12 * fontZoom) labelColor = BLACK if self.dataset.type == "Publish" or self.dataset.type == "Geno": dataset_label = self.dataset.fullname else: dataset_label = "%s - %s" % (self.dataset.group.name, self.dataset.fullname) self.current_datetime = datetime.datetime.now().strftime("%b %d %Y %H:%M:%S") string1 = 'UTC Timestamp: %s' % (self.current_datetime) string2 = 'Dataset: %s' % (dataset_label) string3 = 'Trait Hash: %s' % (self.vals_hash) if self.genofile_string == "": string4 = 'Genotype File: %s.geno' % self.dataset.group.name else: string4 = 'Genotype File: %s' % self.genofile_string.split(":")[1] string6 = '' if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam": if self.use_loco == "True": string5 = 'Using GEMMA mapping method with LOCO and ' else: string5 = 'Using GEMMA mapping method with ' if self.covariates != "": string5 += 'the cofactors below:' cofactor_names = ", ".join( [covar.split(":")[0] for covar in self.covariates.split(",")]) string6 = cofactor_names else: string5 += 'no cofactors' elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno": string5 = 'Using R/qtl mapping method with ' if self.covariates != "": string5 += 'the cofactors below:' cofactor_names = ", ".join( [covar.split(":")[0] for covar in self.covariates.split(",")]) string6 = cofactor_names elif self.controlLocus and self.doControl != "false": string5 += '%s as control' % self.controlLocus else: string5 += 'no cofactors' else: string5 = 'Using Haldane mapping function with ' if self.controlLocus and self.doControl != "false": string5 += '%s as control' % self.controlLocus else: string5 += 'no control for other QTLs' y_constant = 10 if self.this_trait.name: if self.selectedChr == -1: identification = "Mapping on All Chromosomes for " else: identification = "Mapping on Chromosome %s for " % ( self.ChrList[self.selectedChr][0]) if self.this_trait.symbol: identification += "Trait: %s - %s" % ( self.this_trait.display_name, self.this_trait.symbol) elif self.dataset.type == "Publish": if self.this_trait.post_publication_abbreviation: identification += "Trait: %s - %s" % ( self.this_trait.display_name, self.this_trait.post_publication_abbreviation) elif self.this_trait.pre_publication_abbreviation: identification += "Trait: %s - %s" % ( self.this_trait.display_name, self.this_trait.pre_publication_abbreviation) else: identification += "Trait: %s" % (self.this_trait.display_name) else: identification += "Trait: %s" % (self.this_trait.display_name) identification += " with %s samples" % (self.n_samples) d = 4 + max( im_drawer.textsize(identification, font=labelFont)[0], im_drawer.textsize(string1, font=labelFont)[0], im_drawer.textsize(string2, font=labelFont)[0], im_drawer.textsize(string3, font=labelFont)[0], im_drawer.textsize(string4, font=labelFont)[0]) im_drawer.text( text=identification, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 else: d = 4 + max( im_drawer.textsize(string1, font=labelFont)[0], im_drawer.textsize(string2, font=labelFont)[0], im_drawer.textsize(string3, font=labelFont)[0], im_drawer.textsize(string4, font=labelFont)[0]) if len(self.transform) > 0: transform_text = "Transform - " if self.transform == "qnorm": transform_text += "Quantile Normalized" elif self.transform == "log2" or self.transform == "log10": transform_text += self.transform.capitalize() elif self.transform == "sqrt": transform_text += "Square Root" elif self.transform == "zscore": transform_text += "Z-Score" elif self.transform == "invert": transform_text += "Invert +/-" im_drawer.text( text=transform_text, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 im_drawer.text( text=string1, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 im_drawer.text( text=string2, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 im_drawer.text( text=string3, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 im_drawer.text( text=string4, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 if string4 != '': im_drawer.text( text=string5, xy=(xLeftOffset, y_constant * fontZoom), font=labelFont, fill=labelColor) y_constant += 15 if string5 != '': im_drawer.text( 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): ref_strand = homology_dict["ref_strand"] ref_start = homology_dict["ref_start"] ref_end = homology_dict["ref_end"] query_chr = homology_dict["query_chr"] query_strand = homology_dict["query_strand"] query_start = homology_dict["query_start"] query_end = homology_dict["query_end"] geneLength = (ref_end - ref_start) * 1000.0 tenPercentLength = geneLength * 0.0001 geneStartPix = xLeftOffset + \ plotXScale * (float(ref_start) - startMb) geneEndPix = xLeftOffset + plotXScale * \ (float(ref_end) - startMb) # at least one pixel if (geneEndPix < xLeftOffset): return # this gene is not on the screen if (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 myColor = BLACK outlineColor = myColor fillColor = myColor TITLE = f"hg38: Chr {query_chr} from {query_start:.3f} to {query_end:.3f} Mb" HREF = f"http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr{query_chr}:{int(query_start * 1000000)}-{int(query_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 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 query_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) COORDS = "%d, %d, %d, %d" % ( geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) 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: 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 gIndex, theGO in enumerate(self.geneCol): geneNCBILink = 'http://www.ncbi.nlm.nih.gov/gene?term=%s' if self.dataset.group.species == "mouse": exonStarts = [] exonEnds = [] txStart = theGO["TxStart"] txEnd = theGO["TxEnd"] geneLength = (txEnd - txStart) * 1000.0 tenPercentLength = geneLength * 0.0001 SNPdensity = theGO["snpCount"] / geneLength if theGO['exonStarts']: exonStarts = list( map(float, theGO['exonStarts'].split(",")[:-1])) exonEnds = list(map(float, theGO['exonEnds'].split(",")[:-1])) cdsStart = theGO['cdsStart'] cdsEnd = theGO['cdsEnd'] accession = theGO['NM_ID'] geneSymbol = theGO["GeneSymbol"] strand = theGO["Strand"] exonCount = theGO["exonCount"] geneStartPix = xLeftOffset + \ plotXScale * (float(txStart) - startMb) geneEndPix = xLeftOffset + plotXScale * \ (float(txEnd) - 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 densities = [1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0] if SNPdensity < densities[0]: myColor = BLACK elif SNPdensity < densities[1]: myColor = PURPLE elif SNPdensity < densities[2]: myColor = DARKBLUE elif SNPdensity < densities[3]: myColor = DARKGREEN elif SNPdensity < densities[4]: myColor = GOLD elif SNPdensity < densities[5]: myColor = DARKORANGE else: myColor = DARKRED outlineColor = myColor fillColor = myColor TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % ( geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount) # NL: 06-02-2011 Rob required to change this link for gene related HREF = geneNCBILink % geneSymbol elif self.dataset.group.species == "rat": exonStarts = [] exonEnds = [] txStart = theGO["TxStart"] txEnd = theGO["TxEnd"] cdsStart = theGO["TxStart"] cdsEnd = theGO["TxEnd"] geneSymbol = theGO["GeneSymbol"] strand = theGO["Strand"] exonCount = 0 geneStartPix = xLeftOffset + \ plotXScale * (float(txStart) - startMb) geneEndPix = xLeftOffset + plotXScale * \ (float(txEnd) - 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 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 = ORANGE fillColor = ORANGE TITLE = "Gene: %s" % geneSymbol # Draw Genes geneYLocation = yPaddingTop + \ (gIndex % 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 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 blocks for the exon regions for i in range(0, len(exonStarts)): exonStartPix = ( exonStarts[i] - startMb) * plotXScale + xLeftOffset exonEndPix = (exonEnds[i] - startMb) * \ plotXScale + xLeftOffset if (exonStartPix < xLeftOffset): exonStartPix = xLeftOffset if (exonEndPix < xLeftOffset): exonEndPix = xLeftOffset if (exonEndPix > xLeftOffset + plotWidth): exonEndPix = xLeftOffset + plotWidth if (exonStartPix > xLeftOffset + plotWidth): exonStartPix = xLeftOffset + plotWidth im_drawer.rectangle( xy=((exonStartPix, geneYLocation), (exonEndPix, (geneYLocation + self.EACH_GENE_HEIGHT * zoom))), outline=outlineColor, fill=fillColor) # draw gray blocks for 3' and 5' UTR blocks if cdsStart and cdsEnd: utrStartPix = (txStart - startMb) * \ plotXScale + xLeftOffset utrEndPix = (cdsStart - startMb) * plotXScale + xLeftOffset if (utrStartPix < xLeftOffset): utrStartPix = xLeftOffset if (utrEndPix < xLeftOffset): utrEndPix = xLeftOffset if (utrEndPix > xLeftOffset + plotWidth): utrEndPix = xLeftOffset + plotWidth if (utrStartPix > xLeftOffset + plotWidth): utrStartPix = xLeftOffset + plotWidth if self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB: if strand == "-": labelText = "3'" else: labelText = "5'" im_drawer.text( text=labelText, xy=(utrStartPix - 9, geneYLocation + \ self.EACH_GENE_HEIGHT), font=ImageFont.truetype(font=ARIAL_FILE, size=2)) # the second UTR region utrStartPix = (cdsEnd - startMb) * plotXScale + xLeftOffset utrEndPix = (txEnd - startMb) * plotXScale + xLeftOffset if (utrStartPix < xLeftOffset): utrStartPix = xLeftOffset if (utrEndPix < xLeftOffset): utrEndPix = xLeftOffset if (utrEndPix > xLeftOffset + plotWidth): utrEndPix = xLeftOffset + plotWidth if (utrStartPix > xLeftOffset + plotWidth): utrStartPix = xLeftOffset + plotWidth if self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB: if strand == "-": labelText = "5'" else: labelText = "3'" im_drawer.text( text=labelText, xy=(utrEndPix + 2, geneYLocation + \ self.EACH_GENE_HEIGHT), font=ImageFont.truetype(font=ARIAL_FILE, size=2)) # 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")) # BEGIN HaplotypeAnalyst def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None): if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol: return xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset yPaddingTop = yTopOffset thisTrait = self.this_trait samplelist = list(self.genotype.prgy) smd = [] for sample in self.sample_vals_dict.keys(): if self.sample_vals_dict[sample] != "x" and sample in samplelist: temp = GeneralObject(name=sample, value=float( self.sample_vals_dict[sample])) smd.append(temp) else: continue smd.sort(key=lambda A: A.value) smd.reverse() oldgeneEndPix = -1 # Initializing plotRight, error before plotRight = xRightOffset im_drawer = ImageDraw.Draw(canvas) # find out PlotRight for _chr in self.genotype: if _chr.name == self.ChrList[self.selectedChr][0]: for i, _locus in enumerate(_chr): txStart = _chr[i].Mb txEnd = _chr[i].Mb geneStartPix = xLeftOffset + plotXScale * \ (float(txStart) - startMb) - 0 geneEndPix = xLeftOffset + plotXScale * \ (float(txEnd) - startMb) - 0 drawit = 1 if (geneStartPix < xLeftOffset): drawit = 0 if (geneStartPix > xLeftOffset + plotWidth): drawit = 0 if drawit == 1: if _chr[i].name != " - ": plotRight = geneEndPix + 4 # end find out PlotRight firstGene = 1 lastGene = 0 # Sets the length to the length of the strain list. Beforehand, "oldgeno = self.genotype[0][i].genotype" # was the only place it was initialized, which worked as long as the very start (startMb = None/0) wasn't being mapped. # Now there should always be some value set for "oldgeno" - Zach 12/14/2010 oldgeno = [None] * len(self.strainlist) for i, _chr in enumerate(self.genotype): if _chr.name == self.ChrList[self.selectedChr][0]: for j, _locus in enumerate(_chr): txStart = _chr[j].Mb txEnd = _chr[j].Mb geneStartPix = xLeftOffset + plotXScale * \ (float(txStart) - startMb) - 0 geneEndPix = xLeftOffset + plotXScale * \ (float(txEnd) - startMb) + 0 if oldgeneEndPix >= xLeftOffset: drawStart = oldgeneEndPix + 4 else: drawStart = xLeftOffset + 3 drawEnd = plotRight - 9 drawit = 1 if (geneStartPix < xLeftOffset): if firstGene == 1: drawit = 1 else: drawit = 0 elif (geneStartPix > (xLeftOffset + plotWidth - 3)): if lastGene == 0: drawit = 1 drawEnd = xLeftOffset + plotWidth - 6 lastGene = 1 else: break else: firstGene = 0 drawit = 1 if drawit == 1: myColor = DARKBLUE outlineColor = myColor fillColor = myColor maxind = 0 # Draw Genes geneYLocation = yPaddingTop + 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 if _chr[j].name != " - ": if (firstGene == 1) and (lastGene != 1): oldgeneEndPix = drawStart = xLeftOffset oldgeno = _chr[j].genotype continue for k, _geno in enumerate(_chr[j].genotype): plotbxd = 0 if samplelist[k] in [item.name for item in smd]: plotbxd = 1 if (plotbxd == 1): ind = 0 if samplelist[k] in [item.name for item in smd]: ind = [item.name for item in smd].index( samplelist[k]) maxind = max(ind, maxind) # lines if (oldgeno[k] == -1 and _geno == -1): mylineColor = self.HAPLOTYPE_NEGATIVE elif (oldgeno[k] == 1 and _geno == 1): mylineColor = self.HAPLOTYPE_POSITIVE elif (oldgeno[k] == 0 and _geno == 0): mylineColor = self.HAPLOTYPE_HETEROZYGOUS else: mylineColor = self.HAPLOTYPE_RECOMBINATION # XZ: Unknown im_drawer.line( xy=((drawStart, geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom), (drawEnd, geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom)), fill=mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2)) fillColor = BLACK outlineColor = BLACK if lastGene == 0: im_drawer.rectangle( xy=((geneStartPix, geneYLocation + 2 * ind * self.EACH_GENE_HEIGHT * zoom), (geneEndPix, geneYLocation + 2 * ind * self.EACH_GENE_HEIGHT + 2 * self.EACH_GENE_HEIGHT * zoom)), outline=outlineColor, fill=fillColor) COORDS = "%d, %d, %d, %d" % ( geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT)) TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % ( samplelist[k], _chr[j].name, float(txStart)) HREF = '' gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=COORDS, href=HREF, title=TITLE)) # if there are no more markers in a chromosome, the plotRight value calculated above will be before the plotWidth # resulting in some empty space on the right side of the plot area. This draws an "unknown" bar from plotRight to the edge. if (plotRight < (xLeftOffset + plotWidth - 3)) and (lastGene == 0): drawEnd = xLeftOffset + plotWidth - 6 mylineColor = self.HAPLOTYPE_RECOMBINATION im_drawer.line( xy=((plotRight, geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom), (drawEnd, geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom)), fill=mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2)) if lastGene == 0: draw_rotated_text( canvas, text="%s" % (_chr[j].name), font=ImageFont.truetype(font=VERDANA_FILE, size=12), xy=(geneStartPix, geneYLocation + 17 + 2 * maxind * self.EACH_GENE_HEIGHT * zoom), fill=BLACK, angle=-90) oldgeneEndPix = geneEndPix oldgeno = _chr[j].genotype firstGene = 0 else: lastGene = 0 for i, _chr in enumerate(self.genotype): if _chr.name == self.ChrList[self.selectedChr][0]: for j, _geno in enumerate(_chr[1].genotype): plotbxd = 0 if samplelist[j] in [item.name for item in smd]: plotbxd = 1 if (plotbxd == 1): ind = [item.name for item in smd].index( samplelist[j]) - 1 expr = smd[ind+1].value # Place where font is hardcoded im_drawer.text( text="%s" % (samplelist[j]), xy=((xLeftOffset + plotWidth + 10), geneYLocation + 11 + 2 * ind * self.EACH_GENE_HEIGHT * zoom), font=ImageFont.truetype( font=VERDANA_FILE, size=12), fill=BLACK) im_drawer.text( text="%2.2f" % (expr), xy=((xLeftOffset + plotWidth + 80), geneYLocation + 11 + 2 * ind * self.EACH_GENE_HEIGHT * zoom), font=ImageFont.truetype( font=VERDANA_FILE, size=12), fill=BLACK) # END HaplotypeAnalyst def drawClickBand(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: 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 # only draw this many clickable regions (if you set it higher, you get more precision in clicking, # but it makes the HTML huge, and takes forever to render the page in the first place) # Draw the bands that you can click on to go to UCSC / Ensembl MAX_CLICKABLE_REGION_DIVISIONS = 100 clickableRegionLabelFont = ImageFont.truetype( font=VERDANA_FILE, size=9) pixelStep = max( 5, int(float(plotWidth) / MAX_CLICKABLE_REGION_DIVISIONS)) # pixelStep: every N pixels, we make a new clickable area for the user to go to that area of the genome. numBasesCurrentlyOnScreen = self.kONE_MILLION * \ abs(startMb - endMb) # Number of bases on screen now flankingWidthInBases = int( min((float(numBasesCurrentlyOnScreen) / 2.0), (5 * self.kONE_MILLION))) webqtlZoomWidth = numBasesCurrentlyOnScreen / 16.0 # Flanking width should be such that we either zoom in to a 10 million base region, or we show the clicked region at the same scale as we are currently seeing. currentChromosome = self.genotype[0].name i = 0 paddingTop = yTopOffset phenogenPaddingTop = paddingTop + \ (self.BAND_HEIGHT + self.BAND_SPACING) if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": ucscPaddingTop = paddingTop + 2 * \ (self.BAND_HEIGHT + self.BAND_SPACING) ensemblPaddingTop = paddingTop + 3 * \ (self.BAND_HEIGHT + self.BAND_SPACING) else: ucscPaddingTop = paddingTop + \ (self.BAND_HEIGHT + self.BAND_SPACING) ensemblPaddingTop = paddingTop + 2 * \ (self.BAND_HEIGHT + self.BAND_SPACING) if zoom == 1: for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep): calBase = self.kONE_MILLION * \ (startMb + (endMb - startMb) * \ (pixel - xLeftOffset - 0.0) / plotWidth) xBrowse1 = pixel xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1)) WEBQTL_COORDS = "%d, %d, %d, %d" % ( xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT)) WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max( 0, (calBase - webqtlZoomWidth)) / 1000000.0, (calBase + webqtlZoomWidth) / 1000000.0) WEBQTL_TITLE = "Click to view this section of the genome in WebQTL" gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=WEBQTL_COORDS, href=WEBQTL_HREF, title=WEBQTL_TITLE)) im_drawer.rectangle( xy=((xBrowse1, paddingTop), (xBrowse2, (paddingTop + self.BAND_HEIGHT))), outline=self.CLICKABLE_WEBQTL_REGION_COLOR, fill=self.CLICKABLE_WEBQTL_REGION_COLOR) im_drawer.line( xy=((xBrowse1, paddingTop), (xBrowse1, (paddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR) if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": PHENOGEN_COORDS = "%d, %d, %d, %d" % ( xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % ( self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) else: PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % ( self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen" gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=PHENOGEN_COORDS, href=PHENOGEN_HREF, title=PHENOGEN_TITLE)) im_drawer.rectangle( xy=((xBrowse1, phenogenPaddingTop), (xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT))), outline=self.CLICKABLE_PHENOGEN_REGION_COLOR, fill=self.CLICKABLE_PHENOGEN_REGION_COLOR) im_drawer.line( xy=((xBrowse1, phenogenPaddingTop), (xBrowse1, (phenogenPaddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR) UCSC_COORDS = "%d, %d, %d, %d" % ( xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % ( self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr) else: UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % ( self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser" gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=UCSC_COORDS, href=UCSC_HREF, title=UCSC_TITLE)) im_drawer.rectangle( xy=((xBrowse1, ucscPaddingTop), (xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT))), outline=self.CLICKABLE_UCSC_REGION_COLOR, fill=self.CLICKABLE_UCSC_REGION_COLOR) im_drawer.line( xy=((xBrowse1, ucscPaddingTop), (xBrowse1, (ucscPaddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR) ENSEMBL_COORDS = "%d, %d, %d, %d" % ( xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT)) if self.dataset.group.species == "mouse": ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % ( self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) else: ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % ( self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases) ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser" gifmap.append(HtmlGenWrapper.create_area_tag( shape='rect', coords=ENSEMBL_COORDS, href=ENSEMBL_HREF, title=ENSEMBL_TITLE)) im_drawer.rectangle( xy=((xBrowse1, ensemblPaddingTop), (xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT))), outline=self.CLICKABLE_ENSEMBL_REGION_COLOR, fill=self.CLICKABLE_ENSEMBL_REGION_COLOR) im_drawer.line( xy=((xBrowse1, ensemblPaddingTop), (xBrowse1, (ensemblPaddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR) # end for im_drawer.text( text="Click to view the corresponding section of the genome in an 8x expanded WebQTL map", xy=((xLeftOffset + 10), paddingTop), # + self.BAND_HEIGHT/2), font=clickableRegionLabelFont, fill=self.CLICKABLE_WEBQTL_TEXT_COLOR) if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": im_drawer.text( text="Click to view the corresponding section of the genome in PhenoGen", # + self.BAND_HEIGHT/2), xy=((xLeftOffset + 10), phenogenPaddingTop), font=clickableRegionLabelFont, fill=self.CLICKABLE_PHENOGEN_TEXT_COLOR) im_drawer.text( text="Click to view the corresponding section of the genome in the UCSC Genome Browser", # + self.BAND_HEIGHT/2), xy=((xLeftOffset + 10), ucscPaddingTop), font=clickableRegionLabelFont, fill=self.CLICKABLE_UCSC_TEXT_COLOR) im_drawer.text( text="Click to view the corresponding section of the genome in the Ensembl Genome Browser", # + self.BAND_HEIGHT/2), xy=((xLeftOffset + 10), ensemblPaddingTop), font=clickableRegionLabelFont, fill=self.CLICKABLE_ENSEMBL_TEXT_COLOR) # draw the gray text chrFont = ImageFont.truetype( font=VERDANA_BOLD_FILE, size=26 * zoom) chrX = xLeftOffset + plotWidth - 2 - im_drawer.textsize( "Chr %s" % self.ChrList[self.selectedChr][0], font=chrFont)[0] im_drawer.text( text="Chr %s" % self.ChrList[self.selectedChr][0], xy=(chrX, paddingTop), font=chrFont, fill=GRAY) # end of drawBrowserClickableRegions else: # draw the gray text chrFont = ImageFont.truetype(font=VERDANA_FILE, size=26 * zoom) chrX = xLeftOffset + (plotWidth - im_drawer.textsize( "Chr %s" % currentChromosome, font=chrFont)[0]) / 2 im_drawer.text( text="Chr %s" % currentChromosome, xy=(chrX, 32), font=chrFont, fill=GRAY) # end of drawBrowserClickableRegions pass def drawXAxis(self, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None): im_drawer = ImageDraw.Draw(canvas) 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 # Parameters NUM_MINOR_TICKS = 5 # Number of minor ticks between major ticks X_MAJOR_TICK_THICKNESS = 3 X_MINOR_TICK_THICKNESS = 1 X_AXIS_THICKNESS = 1 * zoom # ======= Alex: Draw the X-axis labels (megabase location) MBLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=15 * zoom) xMajorTickHeight = 10 * zoom # How high the tick extends below the axis xMinorTickHeight = 5 * zoom xAxisTickMarkColor = BLACK xAxisLabelColor = BLACK fontHeight = 12 * fontZoom # How tall the font that we're using is spacingFromLabelToAxis = 10 if self.plotScale == 'physic': strYLoc = yZero + MBLabelFont.font.height / 2 # Physical single chromosome view if self.selectedChr > -1: XScale = Plot.detScale(startMb, endMb) XStart, XEnd, XStep = XScale if XStep < 8: XStep *= 2 spacingAmtX = spacingAmt = (XEnd - XStart) / XStep j = 0 while abs(spacingAmtX - int(spacingAmtX)) >= spacingAmtX / 100.0 and j < 6: j += 1 spacingAmtX *= 10 formatStr = '%%2.%df' % j for counter, _Mb in enumerate(Plot.frange(XStart, XEnd, spacingAmt / NUM_MINOR_TICKS)): if _Mb < startMb or _Mb > endMb: continue Xc = xLeftOffset + plotXScale * (_Mb - startMb) if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark im_drawer.line(xy=((Xc, yZero), (Xc, yZero + xMajorTickHeight)), fill=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark # What Mbase location to put on the label labelStr = str(formatStr % _Mb) strWidth, strHeight = im_drawer.textsize( labelStr, font=MBLabelFont) drawStringXc = (Xc - (strWidth / 2.0)) im_drawer.text(xy=(drawStringXc, strYLoc), text=labelStr, font=MBLabelFont, fill=xAxisLabelColor) else: im_drawer.line(xy=((Xc, yZero), (Xc, yZero + xMinorTickHeight)), fill=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark # Physical genome wide view else: distScale = 0 startPosX = xLeftOffset for i, distLen in enumerate(self.ChrLengthDistList): if distScale == 0: # universal scale in whole genome mapping if distLen > 75: distScale = 25 elif distLen > 30: distScale = 10 else: distScale = 5 for j, tickdists in enumerate(range(distScale, int(ceil(distLen)), distScale)): im_drawer.line( xy=((startPosX + tickdists * plotXScale, yZero), (startPosX + tickdists * plotXScale, yZero + 7)), fill=BLACK, width=1 * zoom) if j % 2 == 0: draw_rotated_text( canvas, text=str(tickdists), font=MBLabelFont, xy=(startPosX + tickdists * plotXScale, yZero + 10 * zoom), fill=BLACK, angle=270) startPosX += (self.ChrLengthDistList[i] + \ self.GraphInterval) * plotXScale megabaseLabelFont = ImageFont.truetype( font=VERDANA_FILE, size=int(18 * zoom * 1.5)) im_drawer.text( text="Megabases", xy=( xLeftOffset + (plotWidth - im_drawer.textsize( "Megabases", font=megabaseLabelFont)[0]) / 2, strYLoc + MBLabelFont.font.height + 10 * (zoom % 2)), font=megabaseLabelFont, fill=BLACK) pass else: strYLoc = yZero + spacingFromLabelToAxis + MBLabelFont.font.height / 2 ChrAInfo = [] preLpos = -1 distinctCount = 0.0 if self.selectedChr == -1: # ZS: If viewing full genome/all chromosomes for i, _chr in enumerate(self.genotype): thisChr = [] Locus0CM = _chr[0].cM nLoci = len(_chr) if nLoci <= 8: for _locus in _chr: if _locus.name != ' - ': if _locus.cM != preLpos: distinctCount += 1 preLpos = _locus.cM thisChr.append( [_locus.name, _locus.cM - Locus0CM]) else: for j in (0, round(nLoci / 4), round(nLoci / 2), round(nLoci * 3 / 4), -1): while _chr[j].name == ' - ': j += 1 if _chr[j].cM != preLpos: distinctCount += 1 preLpos = _chr[j].cM thisChr.append( [_chr[j].name, _chr[j].cM - Locus0CM]) ChrAInfo.append(thisChr) else: for i, _chr in enumerate(self.genotype): if _chr.name == self.ChrList[self.selectedChr][0]: thisChr = [] Locus0CM = _chr[0].cM for _locus in _chr: if _locus.name != ' - ': if _locus.cM != preLpos: distinctCount += 1 preLpos = _locus.cM thisChr.append( [_locus.name, _locus.cM - Locus0CM]) ChrAInfo.append(thisChr) stepA = (plotWidth + 0.0) / distinctCount LRectWidth = 10 LRectHeight = 3 offsetA = -stepA lineColor = LIGHTBLUE startPosX = xLeftOffset for j, ChrInfo in enumerate(ChrAInfo): preLpos = -1 for i, item in enumerate(ChrInfo): Lname, Lpos = item if Lpos != preLpos: offsetA += stepA differ = 1 else: differ = 0 preLpos = Lpos Lpos *= plotXScale if self.selectedChr > -1: Zorder = i % 5 else: Zorder = 0 if differ: im_drawer.line( xy=((startPosX + Lpos, yZero), (xLeftOffset + offsetA,\ yZero + 25)), fill=lineColor) im_drawer.line( xy=((xLeftOffset + offsetA, yZero + 25), (xLeftOffset + offsetA,\ yZero + 40 + Zorder * (LRectWidth + 3))), fill=lineColor) rectColor = ORANGE else: im_drawer.line( xy=((xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3) - 3), (\ xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3))), fill=lineColor) rectColor = DEEPPINK im_drawer.rectangle( xy=((xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3)), (xLeftOffset + offsetA - LRectHeight, yZero + 40 + Zorder * (LRectWidth + 3) + LRectWidth)), outline=rectColor, fill=rectColor, width=0) COORDS = "%d,%d,%d,%d" % (xLeftOffset + offsetA - LRectHeight, yZero + 40 + Zorder * (LRectWidth + 3),\ xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3) + LRectWidth) HREF = "/show_trait?trait_id=%s&dataset=%s" % ( Lname, self.dataset.group.name + "Geno") #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname) Areas = HtmlGenWrapper.create_area_tag( shape='rect', coords=COORDS, href=HREF, target="_blank", title="Locus : {}".format(Lname)) gifmap.append(Areas) # piddle bug if j == 0: im_drawer.line( xy=((startPosX, yZero), (startPosX, yZero + 40)), fill=lineColor) startPosX += (self.ChrLengthDistList[j] + \ self.GraphInterval) * plotXScale centimorganLabelFont = ImageFont.truetype( font=VERDANA_FILE, size=int(18 * zoom * 1.5)) im_drawer.text( text="Centimorgans", xy=(xLeftOffset + (plotWidth - im_drawer.textsize( "Centimorgans", font=centimorganLabelFont)[0]) / 2, strYLoc + MBLabelFont.font.height + 10 * (zoom % 2)), font=centimorganLabelFont, fill=BLACK) im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset + plotWidth, yZero)), fill=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): im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset plotHeight = canvas.size[1] - yTopOffset - yBottomOffset fontZoom = zoom if zoom == 2: fontZoom = 1.5 INTERCROSS = (self.genotype.type == "intercross") # draw the LRS scale # We first determine whether or not we are using a sliding scale. # If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRS_LOD_Max. # LRSTop is then defined to be above the LRS_LOD_Max by enough to add one additional LRSScale increment. # if we are using a set-scale, then we set LRSTop to be the user's value, and LRS_LOD_Max doesn't matter. # ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD if self.lrsMax <= 0: # sliding scale if "lrs_value" in self.qtlresults[0]: LRS_LOD_Max = max([result['lrs_value'] for result in self.qtlresults]) if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP": LRS_LOD_Max = LRS_LOD_Max / self.LODFACTOR if self.permChecked and self.nperm > 0 and not self.multipleInterval: self.significant = min( self.significant / self.LODFACTOR, webqtlConfig.MAXLRS) self.suggestive = min( self.suggestive / self.LODFACTOR, webqtlConfig.MAXLRS) else: if self.permChecked and self.nperm > 0 and not self.multipleInterval: self.significant = min( self.significant, webqtlConfig.MAXLRS) self.suggestive = min( self.suggestive, webqtlConfig.MAXLRS) else: pass else: LRS_LOD_Max = max([result['lod_score'] for result in self.qtlresults]) + 1 if self.LRS_LOD == "LRS": LRS_LOD_Max = LRS_LOD_Max * self.LODFACTOR if self.permChecked and self.nperm > 0 and not self.multipleInterval: self.significant = min( self.significant * self.LODFACTOR, webqtlConfig.MAXLRS) self.suggestive = min( self.suggestive * self.LODFACTOR, webqtlConfig.MAXLRS) else: if self.permChecked and self.nperm > 0 and not self.multipleInterval: self.significant = min( self.significant, webqtlConfig.MAXLRS) self.suggestive = min( self.suggestive, webqtlConfig.MAXLRS) else: pass if self.permChecked and self.nperm > 0 and not self.multipleInterval: LRS_LOD_Max = max(self.significant, LRS_LOD_Max) # genotype trait will give infinite LRS LRS_LOD_Max = min(LRS_LOD_Max, webqtlConfig.MAXLRS) else: LRS_LOD_Max = self.lrsMax # ZS: Needed to pass to genome browser js_data = json.loads(self.js_data) if self.LRS_LOD == "LRS": js_data['max_score'] = LRS_LOD_Max / 4.61 else: js_data['max_score'] = LRS_LOD_Max self.js_data = json.dumps(js_data) LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) LRSLODFont = ImageFont.truetype( font=VERDANA_FILE, size=int(18 * zoom * 1.5)) yZero = yTopOffset + plotHeight LRSHeightThresh = drawAreaHeight AdditiveHeightThresh = drawAreaHeight / 2 DominanceHeightThresh = drawAreaHeight / 2 if LRS_LOD_Max > 100: LRSScale = 20.0 elif LRS_LOD_Max > 20: LRSScale = 5.0 elif LRS_LOD_Max > 7.5: LRSScale = 2.5 else: LRSScale = 1.0 LRSAxisList = Plot.frange(LRSScale, LRS_LOD_Max, LRSScale) # ZS: Convert to int if all axis values are whole numbers all_int = True for item in LRSAxisList: if isinstance(item, int): continue else: all_int = False break # TODO(PIL): Convert from PIL # if all_int: # max_lrs_width = canvas.stringWidth("%d" % LRS_LOD_Max, font=LRSScaleFont) + 40 # else: # max_lrs_width = canvas.stringWidth("%2.1f" % LRS_LOD_Max, font=LRSScaleFont) + 30 # draw the "LRS" or "LOD" string to the left of the axis LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom) LRSLODFont = ImageFont.truetype( font=VERDANA_FILE, size=int(18 * zoom * 1.5)) yZero = yTopOffset + plotHeight # TEXT_X_DISPLACEMENT = -20 #TEXT_Y_DISPLACEMENT = -215 if all_int: TEXT_X_DISPLACEMENT = -12 else: TEXT_X_DISPLACEMENT = -30 if self.LRS_LOD == "-logP": TEXT_Y_DISPLACEMENT = -242 else: TEXT_Y_DISPLACEMENT = -210 draw_rotated_text( canvas, text=self.LRS_LOD, font=LRSLODFont, xy=(xLeftOffset - im_drawer.textsize( "999.99", font=LRSScaleFont)[0] - 15 * (zoom - 1) + TEXT_X_DISPLACEMENT, yZero + TEXT_Y_DISPLACEMENT - 300 * (zoom - 1)), fill=BLACK, angle=90) for item in LRSAxisList: if LRS_LOD_Max == 0.0: LRS_LOD_Max = 0.000001 yTopOffset + 30 * (zoom - 1) yLRS = yZero - (item / LRS_LOD_Max) * LRSHeightThresh im_drawer.line(xy=((xLeftOffset, yLRS), (xLeftOffset - 4, yLRS)), fill=self.LRS_COLOR, width=1 * zoom) if all_int: scaleStr = "%d" % item else: scaleStr = "%2.1f" % item # Draw the LRS/LOD Y axis label TEXT_Y_DISPLACEMENT = -10 im_drawer.text( text=scaleStr, xy=(xLeftOffset - 4 - im_drawer.textsize(scaleStr, font=LRSScaleFont)[0] - 5, yLRS + TEXT_Y_DISPLACEMENT), font=LRSScaleFont, fill=self.LRS_COLOR) if self.permChecked and self.nperm > 0 and not self.multipleInterval: significantY = yZero - self.significant * LRSHeightThresh / LRS_LOD_Max suggestiveY = yZero - self.suggestive * LRSHeightThresh / LRS_LOD_Max # significantY = yZero - self.significant*LRSHeightThresh/LRSAxisList[-1] # suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSAxisList[-1] startPosX = xLeftOffset # "Significant" and "Suggestive" Drawing Routine # ======= Draw the thick lines for "Significant" and "Suggestive" ===== (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...) # 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 = xLeftOffset + plotWidth im_drawer.line( xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, suggestiveY), (rightEdge, suggestiveY)), fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH * zoom # ,clipX=(xLeftOffset, xLeftOffset + plotWidth-2) ) im_drawer.line( xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, significantY), (rightEdge, significantY)), fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH * zoom # , clipX=(xLeftOffset, xLeftOffset + plotWidth-2) ) sugg_coords = "%d, %d, %d, %d" % ( start_pos_x, suggestiveY - 2, rightEdge + 2 * zoom, suggestiveY + 2) sig_coords = "%d, %d, %d, %d" % ( start_pos_x, significantY - 2, rightEdge + 2 * zoom, significantY + 2) if self.LRS_LOD == 'LRS': sugg_title = "Suggestive LRS = %0.2f" % self.suggestive sig_title = "Significant LRS = %0.2f" % self.significant else: sugg_title = "Suggestive LOD = %0.2f" % ( self.suggestive / 4.61) sig_title = "Significant LOD = %0.2f" % ( self.significant / 4.61) Areas1 = HtmlGenWrapper.create_area_tag( shape='rect', coords=sugg_coords, title=sugg_title) Areas2 = HtmlGenWrapper.create_area_tag( shape='rect', coords=sig_coords, title=sig_title) gifmap.append(Areas1) gifmap.append(Areas2) start_pos_x += (chr_length_dist + \ self.GraphInterval) * plotXScale return start_pos_x for i, _chr in enumerate(self.genotype): if self.selectedChr != -1: if _chr.name == self.ChrList[self.selectedChr][0]: startPosX = add_suggestive_significant_lines_and_legend( startPosX, self.ChrLengthDistList[0]) break else: continue else: startPosX = add_suggestive_significant_lines_and_legend( startPosX, self.ChrLengthDistList[i]) if self.multipleInterval: lrsEdgeWidth = 1 else: if self.additiveChecked: additiveMax = max([abs(X['additive']) for X in self.qtlresults]) lrsEdgeWidth = 3 if zoom == 2: lrsEdgeWidth = 2 * lrsEdgeWidth LRSCoordXY = [] AdditiveCoordXY = [] DominanceCoordXY = [] symbolFont = ImageFont.truetype( font=FNT_BS_FILE, size=5) # ZS: For Manhattan Plot previous_chr = 1 previous_chr_as_int = 0 lineWidth = 1 oldStartPosX = 0 startPosX = xLeftOffset for i, qtlresult in enumerate(self.qtlresults): m = 0 thisLRSColor = self.colorCollection[0] if qtlresult['chr'] != previous_chr and self.selectedChr == -1: if self.manhattan_plot != True and len(LRSCoordXY) > 1: draw_open_polygon(canvas, xy=LRSCoordXY, outline=thisLRSColor, width=lrsEdgeWidth) if not self.multipleInterval and self.additiveChecked: plusColor = self.ADDITIVE_COLOR_POSITIVE minusColor = self.ADDITIVE_COLOR_NEGATIVE for k, aPoint in enumerate(AdditiveCoordXY): if k > 0: Xc0, Yc0 = AdditiveCoordXY[k - 1] Xc, Yc = aPoint if (Yc0 - yZero) * (Yc - yZero) < 0: if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: Xcm = (yZero - Yc0) / \ ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), fill=plusColor, width=lineWidth ) im_drawer.line( xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth ) else: im_drawer.line( xy=((Xc0, yZero - (Yc0 - yZero)), (Xcm, yZero)), fill=minusColor, width=lineWidth ) im_drawer.line( xy=((Xcm, yZero), (Xc, Yc)), fill=plusColor, width=lineWidth ) elif (Yc0 - yZero) * (Yc - yZero) > 0: if Yc < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth ) else: im_drawer.line( xy=((Xc0, yZero - (Yc0 - yZero)), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth ) else: minYc = min(Yc - yZero, Yc0 - yZero) if minYc < 0: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth ) else: im_drawer.line( xy=((Xc0, yZero - (Yc0 - yZero)), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth ) LRSCoordXY = [] AdditiveCoordXY = [] previous_chr = qtlresult['chr'] previous_chr_as_int += 1 newStartPosX = ( self.ChrLengthDistList[previous_chr_as_int - 1] + self.GraphInterval) * plotXScale if newStartPosX != oldStartPosX: startPosX += newStartPosX oldStartPosX = newStartPosX # This is because the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used this_chr = str(self.ChrList[self.selectedChr][0]) if self.plotScale != "physic": this_chr = str(self.ChrList[self.selectedChr][1] + 1) if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr: if self.plotScale != "physic" and self.mapping_method == "reaper" and not self.manhattan_plot: start_cm = self.genotype[self.selectedChr - 1][0].cM Xc = startPosX + (qtlresult['cM'] - start_cm) * plotXScale if hasattr(self.genotype, "filler"): if self.genotype.filler: if self.selectedChr != -1: Xc = startPosX + \ (qtlresult['Mb'] - start_cm) * plotXScale else: Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * ( ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale)) else: if self.selectedChr != -1 and qtlresult['Mb'] > endMb: Xc = startPosX + endMb * plotXScale else: if qtlresult['Mb'] - startMb < 0: continue 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; # for any lrs is over than 460(LRS max in this system), it will be reset to 460 yLRS = yZero - (item / LRS_LOD_Max) * LRSHeightThresh 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 / \ (LRS_LOD_Max * self.LODFACTOR) else: 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 / LRS_LOD_Max else: 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 / LRS_LOD_Max else: if self.LRS_LOD == "LRS": Yc = yZero - \ qtlresult['lod_score'] * self.LODFACTOR * \ LRSHeightThresh / LRS_LOD_Max else: Yc = yZero - \ qtlresult['lod_score'] * \ LRSHeightThresh / LRS_LOD_Max if self.manhattan_plot == True: if self.color_scheme == "single": point_color = self.manhattan_single_color elif self.color_scheme == "varied": point_color = DISTINCT_COLOR_LIST[previous_chr_as_int] else: if self.selectedChr == -1 and (previous_chr_as_int % 2 == 1): point_color = RED else: point_color = BLUE im_drawer.text( text="5", xy=( Xc - im_drawer.textsize("5", font=symbolFont)[0] / 2 + 1, Yc - 4), fill=point_color, font=symbolFont) else: LRSCoordXY.append((Xc, Yc)) if not self.multipleInterval and self.additiveChecked: if additiveMax == 0.0: additiveMax = 0.000001 Yc = yZero - qtlresult['additive'] * \ AdditiveHeightThresh / additiveMax AdditiveCoordXY.append((Xc, Yc)) if self.selectedChr != -1 and qtlresult['Mb'] > endMb and endMb != -1: break m += 1 if self.manhattan_plot != True and len(LRSCoordXY) > 1: draw_open_polygon(canvas, xy=LRSCoordXY, outline=thisLRSColor, width=lrsEdgeWidth) if not self.multipleInterval and self.additiveChecked: plusColor = self.ADDITIVE_COLOR_POSITIVE minusColor = self.ADDITIVE_COLOR_NEGATIVE for k, aPoint in enumerate(AdditiveCoordXY): if k > 0: Xc0, Yc0 = AdditiveCoordXY[k - 1] Xc, Yc = aPoint if (Yc0 - yZero) * (Yc - yZero) < 0: if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: Xcm = (yZero - Yc0) / \ ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), fill=plusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( xy=((Xc0, yZero - (Yc0 - yZero)), (Xcm, yZero)), fill=minusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( xy=((Xcm, yZero), (Xc, Yc)), fill=plusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) elif (Yc0 - yZero) * (Yc - yZero) > 0: if Yc < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( xy=((Xc0, yZero - (Yc0 - yZero)), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: minYc = min(Yc - yZero, Yc0 - yZero) if minYc < 0: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( xy=((Xc0, yZero - (Yc0 - yZero)), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) if not self.multipleInterval and INTERCROSS and self.dominanceChecked: plusColor = self.DOMINANCE_COLOR_POSITIVE minusColor = self.DOMINANCE_COLOR_NEGATIVE for k, aPoint in enumerate(DominanceCoordXY): if k > 0: Xc0, Yc0 = DominanceCoordXY[k - 1] Xc, Yc = aPoint if (Yc0 - yZero) * (Yc - yZero) < 0: if Xc == Xc0: # genotype , locus distance is 0 Xcm = Xc else: Xcm = (yZero - Yc0) / \ ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), fill=plusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( xy=((Xc0, yZero - (Yc0 - yZero)), (Xcm, yZero)), fill=minusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) im_drawer.line( xy=((Xcm, yZero), (Xc, Yc)), fill=plusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) elif (Yc0 - yZero) * (Yc - yZero) > 0: if Yc < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( xy=((Xc0, yZero - (Yc0 - yZero)), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: minYc = min(Yc - yZero, Yc0 - yZero) if minYc < 0: im_drawer.line( xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) else: im_drawer.line( xy=((Xc0, yZero - (Yc0 - yZero)), (Xc, yZero - (Yc - yZero))), fill=minusColor, width=lineWidth # , clipX=(xLeftOffset, xLeftOffset + plotWidth) ) # draw additive scale if not self.multipleInterval and self.additiveChecked: additiveScaleFont = ImageFont.truetype( font=VERDANA_FILE, size=16 * zoom) additiveScale = Plot.detScaleOld(0, additiveMax) additiveStep = (additiveScale[1] - \ additiveScale[0]) / additiveScale[2] additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep) addPlotScale = AdditiveHeightThresh / additiveMax TEXT_Y_DISPLACEMENT = -8 additiveAxisList.append(additiveScale[1]) for item in additiveAxisList: additiveY = yZero - item * addPlotScale im_drawer.line( xy=((xLeftOffset + plotWidth, additiveY), (xLeftOffset + 4 + plotWidth, additiveY)), fill=self.ADDITIVE_COLOR_POSITIVE, width=1 * zoom) scaleStr = "%2.3f" % item im_drawer.text( text=scaleStr, xy=(xLeftOffset + plotWidth + 6, additiveY + TEXT_Y_DISPLACEMENT), font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE) im_drawer.line( xy=((xLeftOffset + plotWidth, additiveY), (xLeftOffset + plotWidth, yZero)), fill=self.ADDITIVE_COLOR_POSITIVE, width=1 * zoom) im_drawer.line( xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30 * (zoom - 1))), fill=self.LRS_COLOR, width=1 * zoom) # the blue line running up the y axis def drawGraphBackground(self, canvas, gifmap, offset=(80, 120, 80, 50), zoom=1, startMb=None, endMb=None): # conditions # multiple Chromosome view # single Chromosome Physical # single Chromosome Genetic im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset plotHeight = canvas.size[1] - yTopOffset - yBottomOffset yBottom = yTopOffset + plotHeight fontZoom = zoom if zoom == 2: fontZoom = 1.5 yTopOffset += 30 # calculate plot scale if self.plotScale != 'physic': self.ChrLengthDistList = self.ChrLengthCMList drawRegionDistance = self.ChrLengthCMSum else: self.ChrLengthDistList = self.ChrLengthMbList drawRegionDistance = self.ChrLengthMbSum if self.selectedChr > -1: # single chromosome view spacingAmt = plotWidth / 13.5 i = 0 for startPix in Plot.frange(xLeftOffset, xLeftOffset + plotWidth, spacingAmt): if (i % 2 == 0): theBackColor = self.GRAPH_BACK_DARK_COLOR else: theBackColor = self.GRAPH_BACK_LIGHT_COLOR i += 1 im_drawer.rectangle( [(startPix, yTopOffset), (min(startPix + spacingAmt, xLeftOffset + plotWidth), yBottom)], outline=theBackColor, fill=theBackColor) drawRegionDistance = self.ChrLengthDistList[self.ChrList[self.selectedChr][1]] self.ChrLengthDistList = [drawRegionDistance] if self.plotScale == 'physic': plotXScale = plotWidth / (endMb - startMb) else: plotXScale = plotWidth / drawRegionDistance else: # multiple chromosome view plotXScale = plotWidth / \ ((len(self.genotype) - 1) * self.GraphInterval + drawRegionDistance) startPosX = xLeftOffset if fontZoom == 1.5: chrFontZoom = 2 else: chrFontZoom = 1 chrLabelFont = ImageFont.truetype( font=VERDANA_FILE, size=24 * chrFontZoom) for i, _chr in enumerate(self.genotype): if (i % 2 == 0): theBackColor = self.GRAPH_BACK_DARK_COLOR else: theBackColor = self.GRAPH_BACK_LIGHT_COLOR # draw the shaded boxes and the sig/sug thick lines im_drawer.rectangle( ((startPosX, yTopOffset), (startPosX + self.ChrLengthDistList[i] * plotXScale, yBottom)), outline=GAINSBORO, fill=theBackColor) chrNameWidth, chrNameHeight = im_drawer.textsize( _chr.name, font=chrLabelFont) chrStartPix = startPosX + \ (self.ChrLengthDistList[i] * plotXScale - chrNameWidth) / 2 chrEndPix = startPosX + \ (self.ChrLengthDistList[i] * plotXScale + chrNameWidth) / 2 TEXT_Y_DISPLACEMENT = 0 im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT), text=_chr.name, font=chrLabelFont, fill=BLACK) COORDS = "%d,%d,%d,%d" % ( chrStartPix, yTopOffset, chrEndPix, yTopOffset + 20) # add by NL 09-03-2010 HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList) Areas = HtmlGenWrapper.create_area_tag( shape='rect', coords=COORDS, href=HREF) gifmap.append(Areas) startPosX += (self.ChrLengthDistList[i] + \ self.GraphInterval) * plotXScale return plotXScale def drawPermutationHistogram(self): ######################################### # Permutation Graph ######################################### myCanvas = Image.new("RGBA", size=(500, 300)) if 'lod_score' in self.qtlresults[0] and self.LRS_LOD == "LRS": perm_output = [value * 4.61 for value in self.perm_output] elif 'lod_score' not in self.qtlresults[0] and self.LRS_LOD == "LOD": perm_output = [value / 4.61 for value in self.perm_output] else: perm_output = self.perm_output filename = webqtlUtil.genRandStr("Reg_") Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, YLabel='Frequency', title=' Histogram of Permutation Test') myCanvas.save("{}.gif".format(GENERATED_IMAGE_DIR + filename), format='gif') return filename def geneTable(self, geneCol, refGene=None): if self.dataset.group.species == 'mouse' or self.dataset.group.species == 'rat': self.gene_table_header = self.getGeneTableHeaderList(refGene=None) self.gene_table_body = self.getGeneTableBody(geneCol, refGene=None) else: self.gene_table_header = None self.gene_table_body = None def getGeneTableHeaderList(self, refGene=None): gene_table_header_list = [] if self.dataset.group.species == "mouse": if refGene: gene_table_header_list = ["Index", "Symbol", "Mb Start", "Length (Kb)", "SNP Count", "SNP Density", "Avg Expr", "Human Chr", "Mb Start (hg19)", "Literature Correlation", "Gene Description"] else: gene_table_header_list = ["", "Index", "Symbol", "Mb Start", "Length (Kb)", "SNP Count", "SNP Density", "Avg Expr", "Human Chr", "Mb Start (hg19)", "Gene Description"] elif self.dataset.group.species == "rat": gene_table_header_list = ["", "Index", "Symbol", "Mb Start", "Length (Kb)", "Avg Expr", "Mouse Chr", "Mb Start (mm9)", "Human Chr", "Mb Start (hg19)", "Gene Description"] return gene_table_header_list def getGeneTableBody(self, geneCol, refGene=None): gene_table_body = [] tableIterationsCnt = 0 if self.dataset.group.species == "mouse": for gIndex, theGO in enumerate(geneCol): tableIterationsCnt = tableIterationsCnt + 1 this_row = [] # container for the cells of each row selectCheck = HtmlGenWrapper.create_input_tag( type_="checkbox", name="selectCheck", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") # checkbox for each row geneLength = (theGO["TxEnd"] - theGO["TxStart"]) * 1000.0 tenPercentLength = geneLength * 0.0001 txStart = theGO["TxStart"] txEnd = theGO["TxEnd"] theGO["snpDensity"] = theGO["snpCount"] / geneLength if self.ALEX_DEBUG_BOOL_PRINT_GENE_LIST: geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO[ "GeneID"] if theGO["snpCount"]: snpString = HT.Link( (f"http://genenetwork.org/webqtl/main.py?FormID=snpBrowser&" f"chr={theGO['Chr']}&" f"start={theGO['TxStart']}&" f"end={theGO['TxEnd']}&" f"geneName={theGO['GeneSymbol']}&" f"s1={self.diffCol[0]}&s2=%d"), str(theGO["snpCount"]) # The text to display ) snpString.set_blank_target() snpString.set_attribute("class", "normalsize") else: snpString = 0 mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm10&position=chr" + \ theGO["Chr"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str( int(theGO["TxEnd"] * 1000000.0)) + "&pix=620&Submit=submit" # the chromosomes for human 1 are 1qXX.XX if 'humanGene' in theGO: if theGO['humanGene']["TxStart"] == '': humanStartDisplay = "" else: humanStartDisplay = "%0.6f" % theGO['humanGene']["TxStart"] humanChr = theGO['humanGene']["Chr"] humanTxStart = theGO['humanGene']["TxStart"] humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % ( humanChr, int(1000000 * theGO['humanGene']["TxStart"]), int(1000000 * theGO['humanGene']["TxEnd"])) else: humanStartString = humanChr = humanStartDisplay = "--" geneDescription = theGO["GeneDescription"] if len(geneDescription) > 70: geneDescription = geneDescription[:70] + "..." if theGO["snpDensity"] < 0.000001: snpDensityStr = "0" else: snpDensityStr = "%0.6f" % theGO["snpDensity"] avgExpr = [] # theGO["avgExprVal"] if avgExpr in ([], None): avgExpr = "--" else: avgExpr = "%0.6f" % avgExpr # If we have a referenceGene then we will show the Literature Correlation if theGO["Chr"] == "X": chr_as_int = 19 else: chr_as_int = int(theGO["Chr"]) - 1 if refGene: literatureCorrelationString = str(self.getLiteratureCorrelation( self.cursor, refGene, theGO['GeneID']) or "N/A") this_row = [selectCheck.__str__(), str(tableIterationsCnt), str(HtmlGenWrapper.create_link_tag( geneIdString, theGO["GeneSymbol"], target="_blank") ), str(HtmlGenWrapper.create_link_tag( mouseStartString, "{:.6f}".format(txStart), target="_blank") ), str(HtmlGenWrapper.create_link_tag( "javascript:rangeView('{}', {:f}, {:f})".format( str(chr_as_int), txStart - tenPercentLength, txEnd + tenPercentLength), "{:.3f}".format(geneLength))), snpString, snpDensityStr, avgExpr, humanChr, str(HtmlGenWrapper.create_link_tag( humanStartString, humanStartDisplay, target="_blank")), literatureCorrelationString, geneDescription] else: this_row = [selectCheck.__str__(), str(tableIterationsCnt), str(HtmlGenWrapper.create_link_tag( geneIdString, theGO["GeneSymbol"], target="_blank")), str(HtmlGenWrapper.create_link_tag( mouseStartString, "{:.6f}".format(txStart), target="_blank")), str(HtmlGenWrapper.create_link_tag( "javascript:rangeView('{}', {:f}, {:f})".format( str(chr_as_int), txStart - tenPercentLength, txEnd + tenPercentLength), "{:.3f}".format(geneLength))), snpString, snpDensityStr, avgExpr, humanChr, str(HtmlGenWrapper.create_link_tag( humanStartString, humanStartDisplay, target="_blank")), geneDescription] gene_table_body.append(this_row) elif self.dataset.group.species == 'rat': for gIndex, theGO in enumerate(geneCol): this_row = [] # container for the cells of each row selectCheck = str(HtmlGenWrapper.create_input_tag( type_="checkbox", name="selectCheck", Class="checkbox trait_checkbox")) # checkbox for each row if theGO["GeneID"] != "": geneSymbolNCBI = str(HtmlGenWrapper.create_link_tag( "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={}".format( theGO["GeneID"]), theGO["GeneSymbol"], Class="normalsize", target="_blank")) else: geneSymbolNCBI = theGO["GeneSymbol"] if theGO["Chr"] == "X": chr_as_int = 20 else: chr_as_int = int(theGO["Chr"]) - 1 geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"])) geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chr"], float( theGO["TxStart"]) - (geneLength * 0.1), float(theGO["TxEnd"]) + (geneLength * 0.1)) avgExprVal = [] if avgExprVal != "" and avgExprVal: avgExprVal = "%0.5f" % float(avgExprVal) else: avgExprVal = "" # Mouse Gene if theGO['mouseGene']: mouseChr = theGO['mouseGene']["Chr"] mouseTxStart = "%0.6f" % theGO['mouseGene']["TxStart"] else: mouseChr = mouseTxStart = "" # the chromosomes for human 1 are 1qXX.XX if 'humanGene' in theGO: humanChr = theGO['humanGene']["Chr"] humanTxStart = "%0.6f" % theGO['humanGene']["TxStart"] else: humanChr = humanTxStart = "" geneDesc = theGO["GeneDescription"] if geneDesc == "---": geneDesc = "" this_row = [selectCheck.__str__(), str(gIndex + 1), geneSymbolNCBI, "%0.6f" % theGO["TxStart"], str(HtmlGenWrapper.create_link_tag( geneLengthURL, "{:.3f}".format(geneLength * 1000.0))), avgExprVal, mouseChr, mouseTxStart, humanChr, humanTxStart, geneDesc] gene_table_body.append(this_row) return gene_table_body def getLiteratureCorrelation(cursor, geneId1=None, geneId2=None): if not geneId1 or not geneId2: return None if geneId1 == geneId2: return 1.0 geneId1 = str(geneId1) geneId2 = str(geneId2) lCorr = None try: query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s' for x, y in [(geneId1, geneId2), (geneId2, geneId1)]: cursor.execute(query, (x, y)) lCorr = cursor.fetchone() if lCorr: lCorr = lCorr[0] break except: raise # lCorr = None return lCorr