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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/heatmap/heatmapPage.py
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'web/webqtl/heatmap/heatmapPage.py')
-rwxr-xr-xweb/webqtl/heatmap/heatmapPage.py116
1 files changed, 0 insertions, 116 deletions
diff --git a/web/webqtl/heatmap/heatmapPage.py b/web/webqtl/heatmap/heatmapPage.py
deleted file mode 100755
index b407b0c8..00000000
--- a/web/webqtl/heatmap/heatmapPage.py
+++ /dev/null
@@ -1,116 +0,0 @@
-# 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 GeneNetwork Core Team 2010/10/20
-
-import os
-import string
-from htmlgen import HTMLgen2 as HT
-
-from base.templatePage import templatePage
-from base import webqtlConfig
-from heatmap.Heatmap import Heatmap
-
-
-# XZ, 09/09/2008: After adding several traits to collection, click "QTL Heatmap" button,
-# XZ, 09/09/2008: This class will generate what you see.
-#########################################
-# QTL heatmap Page
-#########################################
-class heatmapPage(templatePage):
-
- def __init__(self,fd):
-
- templatePage.__init__(self, fd)
-
- if not self.openMysql():
- return
- if not fd.genotype:
- fd.readGenotype()
-
- searchResult = fd.formdata.getvalue('searchResult')
- if not searchResult:
- heading = 'QTL Heatmap'
- detail = ['You need to select at least two traits in order to generate QTL heatmap.']
- self.error(heading=heading,detail=detail)
- return
- if type("1") == type(searchResult):
- searchResult = string.split(searchResult,'\t')
- if searchResult:
- if len(searchResult) > webqtlConfig.MAXCORR:
- heading = 'QTL Heatmap'
- detail = ['In order to display the QTL heat map properly, do not select more than %d traits for analysis.' % webqtlConfig.MAXCORR]
- self.error(heading=heading,detail=detail)
- return
- else:
- heading = 'QTL Heatmap'
- detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')]
- self.error(heading=heading,detail=detail)
- return
- self.dict['title'] = 'QTL heatmap'
- NNN = len(searchResult)
- if NNN == 0:
- heading = "QTL Heatmap"
- detail = ['No trait was selected for %s data set. No QTL heatmap was generated.' % fd.RISet]
- self.error(heading=heading,detail=detail)
- return
- elif NNN < 2:
- heading = 'QTL Heatmap'
- detail = ['You need to select at least two traits in order to generate QTL heatmap.']
- self.error(heading=heading,detail=detail)
- return
- else:
- colorScheme = fd.formdata.getvalue('colorScheme')
- if not colorScheme:
- colorScheme = '1'
- heatmapObject = Heatmap(fd=fd, searchResult=searchResult, colorScheme=colorScheme, userPrivilege=self.privilege, userName=self.userName)
- filename, areas, sessionfile = heatmapObject.getResult()
- gifmap = HT.Map(name='traitMap')
- for area in areas:
- Areas = HT.Area(shape='rect', coords=area[0], href=area[1], title=area[2])
- gifmap.areas.append(Areas)
- img2=HT.Image('/image/'+filename+'.png',border=0,usemap='#traitMap')
- imgUrl = 'Right-click or control-click on the link to download this graph as a <a href="/image/%s.png" class="normalsize" target="_blank">PNG file</a>' % filename
- form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
- hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_','RISet':fd.RISet,'searchResult':string.join(searchResult,'\t')}
- if fd.incparentsf1:
- hddn['incparentsf1']='ON'
- for key in hddn.keys():
- form.append(HT.Input(name=key, value=hddn[key], type='hidden'))
- heatmapButton = HT.Input(type='button' ,name='mintmap',value='Redraw QTL Heatmap', onClick="databaseFunc(this.form,'heatmap');",Class="button")
- spects = {'0':'Single Spectrum','1':'Grey + Blue + Red','2':'Blue + Red'}
- schemeMenu = HT.Select(name='colorScheme')
- schemeMenu.append(('Single Spectrum',0))
- schemeMenu.append(('Grey + Blue + Red',1))
- schemeMenu.append(('Blue + Red',2))
- schemeMenu.selected.append(spects[colorScheme])
- clusterCheck= HT.Input(type='checkbox', Class='checkbox', name='clusterCheck',checked=0)
- targetDescriptionCheck = HT.Input(type='checkbox', Class='checkbox', name='targetDescriptionCheck',checked=0)
- form.append(gifmap,schemeMenu, heatmapButton, HT.P(), clusterCheck, ' Cluster traits ', targetDescriptionCheck, ' Add description', HT.P(),img2, HT.P(), imgUrl)
- form.append(HT.Input(name='session', value=sessionfile, type='hidden'))
- heatmapHelp = HT.Input(type='button' ,name='heatmapHelpButton',value='Info', onClick="openNewWin('/heatmap.html');",Class="button")
- heatmapHeading = HT.Paragraph('QTL Heatmap ', heatmapHelp, Class="title")
- TD_LR = HT.TD(colspan=2,height=200,width="100%",bgColor='#eeeeee')
- TD_LR.append(heatmapHeading, HT.P(),HT.P(),HT.P(),HT.P(),HT.P(),form)
- self.dict['body'] = str(TD_LR)