diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 82 |
1 files changed, 41 insertions, 41 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 3943a401..5925c38f 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -24,13 +24,13 @@ # # Last updated by Zach 12/14/2010 -import datetime import string from math import * -from PIL import (Image,ImageDraw,ImageFont,ImageColor) -import sys,os -import cPickle -import httplib +from PIL import Image +from PIL import ImageDraw +from PIL import ImageFont +from PIL import ImageColor +import os import json from flask import Flask, g @@ -40,15 +40,14 @@ from htmlgen import HTMLgen2 as HT from base import webqtlConfig from base.GeneralObject import GeneralObject from utility import webqtlUtil -from utility import helper_functions from utility import Plot from utility.benchmark import Bench from wqflask.interval_analyst import GeneUtil -from base.webqtlConfig import GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR +from base.webqtlConfig import GENERATED_IMAGE_DIR from utility.pillow_utils import draw_rotated_text, draw_open_polygon import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) RED = ImageColor.getrgb("red") BLUE = ImageColor.getrgb("blue") @@ -80,22 +79,18 @@ ARIAL_FILE = "./wqflask/static/fonts/arial.ttf" assert(os.path.isfile(VERDANA_FILE)) -# ---- END: FONT FILES ---- # -######################################### -# Inteval Mapping Plot Page -######################################### class DisplayMappingResults(object): + """Inteval Mapping Plot Page""" cMGraphInterval = 5 GRAPH_MIN_WIDTH = 900 - GRAPH_MAX_WIDTH = 10000 # Don't set this too high + 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 -=-=-= @@ -106,22 +101,24 @@ class DisplayMappingResults(object): BAND_HEIGHT = 10 BAND_HEIGHT = 10 - NUM_GENE_ROWS = 10 - EACH_GENE_HEIGHT = 6 # number of pixels tall, for each gene to display + 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 = HT.Image('/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. + + # 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 + # BEGIN HaplotypeAnalyst NR_INDIVIDUALS = 0 - ## END HaplotypeAnalyst + # END HaplotypeAnalyst ALEX_DEBUG_BOOL_PRINT_GENE_LIST = 1 @@ -129,13 +126,13 @@ class DisplayMappingResults(object): LODFACTOR = 4.61 - SNP_COLOR = ORANGE # Color for the SNP "seismograph" + 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 + LRS_COLOR = ImageColor.getrgb("#0000FF") + SIGNIFICANT_COLOR = ImageColor.getrgb("#EBC7C7") + SUGGESTIVE_COLOR = GAINSBORO SIGNIFICANT_WIDTH = 5 SUGGESTIVE_WIDTH = 5 ADDITIVE_COLOR_POSITIVE = GREEN @@ -143,33 +140,33 @@ class DisplayMappingResults(object): DOMINANCE_COLOR_POSITIVE = DARKVIOLET DOMINANCE_COLOR_NEGATIVE = RED - ## BEGIN HaplotypeAnalyst + # BEGIN HaplotypeAnalyst HAPLOTYPE_POSITIVE = GREEN HAPLOTYPE_NEGATIVE = RED HAPLOTYPE_HETEROZYGOUS = BLUE HAPLOTYPE_RECOMBINATION = DARKGRAY - ## END HaplotypeAnalyst + # END HaplotypeAnalyst TOP_RIGHT_INFO_COLOR = BLACK - CLICKABLE_WEBQTL_REGION_COLOR = ImageColor.getrgb("#F5D3D3") + CLICKABLE_WEBQTL_REGION_COLOR = ImageColor.getrgb("#F5D3D3") CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = ImageColor.getrgb("#FCE9E9") - CLICKABLE_WEBQTL_TEXT_COLOR = ImageColor.getrgb("#912828") + CLICKABLE_WEBQTL_TEXT_COLOR = ImageColor.getrgb("#912828") - CLICKABLE_PHENOGEN_REGION_COLOR = ImageColor.getrgb("#A2FB94") + CLICKABLE_PHENOGEN_REGION_COLOR = ImageColor.getrgb("#A2FB94") CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR = ImageColor.getrgb("#CEFEC7") - CLICKABLE_PHENOGEN_TEXT_COLOR = ImageColor.getrgb("#1FD504") + CLICKABLE_PHENOGEN_TEXT_COLOR = ImageColor.getrgb("#1FD504") - CLICKABLE_UCSC_REGION_COLOR = ImageColor.getrgb("#DDDDEE") + CLICKABLE_UCSC_REGION_COLOR = ImageColor.getrgb("#DDDDEE") CLICKABLE_UCSC_REGION_OUTLINE_COLOR = ImageColor.getrgb("#EDEDFF") - CLICKABLE_UCSC_TEXT_COLOR = ImageColor.getrgb("#333366") + CLICKABLE_UCSC_TEXT_COLOR = ImageColor.getrgb("#333366") - CLICKABLE_ENSEMBL_REGION_COLOR = ImageColor.getrgb("#EEEEDD") + CLICKABLE_ENSEMBL_REGION_COLOR = ImageColor.getrgb("#EEEEDD") CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR = ImageColor.getrgb("#FEFEEE") - CLICKABLE_ENSEMBL_TEXT_COLOR = ImageColor.getrgb("#555500") + CLICKABLE_ENSEMBL_TEXT_COLOR = ImageColor.getrgb("#555500") GRAPH_BACK_LIGHT_COLOR = ImageColor.getrgb("#FBFBFF") - GRAPH_BACK_DARK_COLOR = ImageColor.getrgb("#F1F1F9") + GRAPH_BACK_DARK_COLOR = ImageColor.getrgb("#F1F1F9") HELP_PAGE_REF = '/glossary.html' @@ -196,7 +193,8 @@ class DisplayMappingResults(object): self.temp_trait = "True" self.group = start_vars['group'] - #Needing for form submission when doing single chr mapping or remapping after changing options + # Needing for form submission when doing single chr + # mapping or remapping after changing options self.samples = start_vars['samples'] self.vals = start_vars['vals'] self.transform = start_vars['transform'] @@ -207,9 +205,9 @@ class DisplayMappingResults(object): self.mapmodel_rqtl_geno = start_vars['model'] self.pair_scan = start_vars['pair_scan'] - #if self.mapping_method != "gemma" and self.mapping_method != "plink": self.js_data = start_vars['js_data'] - self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table + # Top markers to display in table + self.trimmed_markers = start_vars['trimmed_markers'] if self.dataset.group.species == "rat": self._ucscDb = "rn6" @@ -221,7 +219,7 @@ class DisplayMappingResults(object): ##################################### # Options ##################################### - #Mapping options + # Mapping options if start_vars['mapping_scale'] != "": self.plotScale = start_vars['mapping_scale'] else: @@ -542,10 +540,12 @@ class DisplayMappingResults(object): ################################################################ # footnote goes here ################################################################ - btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available 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(HT.BR(), '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.') + 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, 20, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""): im_drawer = ImageDraw.Draw(canvas) |