def expression_boxplot(request, cancer_type, data_set_id, platform_id):
path = bdata.get_data_path_if_exists(data_set_id, platform_id,
'expression')
if path is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {
'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {
'id': data_set_id,
'meta': bdata.data_sources[data_set_id]
},
'cancer_data_sets': cancer_data_sets,
'current_platform': {
'id': platform_id,
'name': bdata.platforms[platform_id]
},
'current_data_type': 'expression',
'default_gene': 'TP53'
}
return render_to_response('gene_boxplot.html',
context,
context_instance=RequestContext(request))
def feature_matrix_plot(request, cancer_type, data_set_id, platform_id):
file_name = bdata.get_data_path_if_exists(data_set_id, platform_id,
'feature_matrix')
if file_name is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {
'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {
'id': data_set_id,
'meta': bdata.data_sources[data_set_id]
},
'cancer_data_sets': cancer_data_sets,
'current_platform': {
'id': platform_id,
'name': bdata.platforms[platform_id]
},
'current_data_type': 'feature_matrix'
}
return render_to_response('feature_matrix.html',
context,
context_instance=RequestContext(request))
def all_platforms_list(request):
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
probesets = bdata.get_probesets_by_platform()
context = {'cancer_data_sets': cancer_data_sets, 'probesets': probesets}
return render_to_response('all_platforms.html',
context,
context_instance=RequestContext(request))
def all_platforms_list(request):
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
probesets = bdata.get_probesets_by_platform()
context = {'cancer_data_sets': cancer_data_sets,
'probesets': probesets}
return render_to_response('all_platforms.html',
context,
context_instance=RequestContext(request))
def cancer_type_data_sets(request, cancer_type):
if cancer_type not in bdata.cancer_types:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'cancer_data_sets': cancer_data_sets}
return render_to_response('data_set_list.html',
context,
context_instance=RequestContext(request))
def set_platform_list(request, cancer_type, data_set_id):
if data_set_id not in bdata.data_sources:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {'id': data_set_id, 'meta': bdata.data_sources[data_set_id]},
'cancer_data_sets': cancer_data_sets}
return render_to_response('data_set_platforms.html',
context,
context_instance=RequestContext(request))
def cancer_type_data_sets(request, cancer_type):
if cancer_type not in bdata.cancer_types:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {
'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'cancer_data_sets': cancer_data_sets
}
return render_to_response('data_set_list.html',
context,
context_instance=RequestContext(request))
def probeset_design_plot(request, platform_id, transcriptome):
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
probesets = bdata.get_probesets_by_platform()
context = {'current_platform': {'id': platform_id, 'name': bdata.platforms[platform_id]},
'cancer_data_sets': cancer_data_sets,
'transcriptome': {'id': transcriptome, 'name': bdata.transcriptomes[transcriptome]},
'probesets': probesets,
'current_data_type': 'probeset_design'}
return render_to_response('probeset_design.html',
context,
context_instance=RequestContext(request))
def expression_boxplot(request, cancer_type, data_set_id, platform_id):
path = bdata.get_data_path_if_exists(data_set_id, platform_id, 'expression')
if path is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {'id': data_set_id, 'meta': bdata.data_sources[data_set_id]},
'cancer_data_sets': cancer_data_sets,
'current_platform': {'id': platform_id, 'name': bdata.platforms[platform_id]},
'current_data_type': 'expression',
'default_gene': 'TP53'}
return render_to_response('gene_boxplot.html',
context,
context_instance=RequestContext(request))
def feature_matrix_plot(request, cancer_type, data_set_id, platform_id):
file_name = bdata.get_data_path_if_exists(data_set_id, platform_id, 'feature_matrix')
if file_name is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {'id': data_set_id, 'meta': bdata.data_sources[data_set_id]},
'cancer_data_sets': cancer_data_sets,
'current_platform': {'id': platform_id, 'name': bdata.platforms[platform_id]},
'current_data_type': 'feature_matrix'}
return render_to_response('feature_matrix.html',
context,
context_instance=RequestContext(request))
def kaplan_meier_plot(request, cancer_type, data_set_id, platform_id):
path = bdata.get_data_path_if_exists(data_set_id, platform_id, 'survival')
if path is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {'id': data_set_id, 'meta': bdata.data_sources[data_set_id]},
'cancer_data_sets': cancer_data_sets,
'current_platform': {'id': platform_id, 'name': bdata.platforms[platform_id]},
'current_data_type': 'survival'}
return render_to_response('gene_survival.html',
context,
context_instance=RequestContext(request))
def set_platform_list(request, cancer_type, data_set_id):
if data_set_id not in bdata.data_sources:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {
'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {
'id': data_set_id,
'meta': bdata.data_sources[data_set_id]
},
'cancer_data_sets': cancer_data_sets
}
return render_to_response('data_set_platforms.html',
context,
context_instance=RequestContext(request))
def probeset_design_plot(request, platform_id, transcriptome):
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
probesets = bdata.get_probesets_by_platform()
context = {
'current_platform': {
'id': platform_id,
'name': bdata.platforms[platform_id]
},
'cancer_data_sets': cancer_data_sets,
'transcriptome': {
'id': transcriptome,
'name': bdata.transcriptomes[transcriptome]
},
'probesets': probesets,
'current_data_type': 'probeset_design'
}
return render_to_response('probeset_design.html',
context,
context_instance=RequestContext(request))
def kaplan_meier_plot(request, cancer_type, data_set_id, platform_id):
path = bdata.get_data_path_if_exists(data_set_id, platform_id, 'survival')
if path is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {
'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {
'id': data_set_id,
'meta': bdata.data_sources[data_set_id]
},
'cancer_data_sets': cancer_data_sets,
'current_platform': {
'id': platform_id,
'name': bdata.platforms[platform_id]
},
'current_data_type': 'survival'
}
return render_to_response('gene_survival.html',
context,
context_instance=RequestContext(request))
def cancer_type_list(request):
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
return render_to_response('cancer_types.html',
{'cancer_data_sets': cancer_data_sets},
context_instance=RequestContext(request))
def cancer_type_list(request):
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
return render_to_response('cancer_types.html',
{'cancer_data_sets': cancer_data_sets},
context_instance=RequestContext(request))
