Interactive multi-omics data explorer to integrate and interactively explore transcripts, proteins and metabolites data.
Home Page: https://graphomics.glasgowcompbio.org/
License: MIT License
![dependabot[bot] avatar](https://avatars.githubusercontent.com/in/29110?v=4 "dependabot[bot]")
Now it's very plain
For small p-values, it's better to format in scientific notations. Now it's rounded to 6 decimal places, but for very small p-values they become 0.000000.
We need an exporting function
Maybe the case and control are reversed.
Store them in environmental variables. Same goes for PALS.
Sometimes the p-values for a transcript pathway analysis are missing, even though a given transcript is on the pathway. See screenshot for example. If this is a least one transcript on the pathway, shouldn't there also be a p-value?
When uploading an analysis, the following stack trace occurs.
Internal Server Error: /linker/upload_analysis
Traceback (most recent call last):
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/exception.py", line 34, in inner
response = get_response(request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 115, in _get_response
response = self.process_exception_by_middleware(e, request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 113, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/views/generic/base.py", line 71, in view
return self.dispatch(request, *args, **kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/views/generic/base.py", line 97, in dispatch
return handler(request, *args, **kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/views/generic/edit.py", line 142, in post
return self.form_valid(form)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/create_analysis_view.py", line 59, in form_valid
species_list, metabolic_pathway_only)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/create_analysis_view.py", line 125, in get_data
results, species_list, current_user, metabolic_pathway_only)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/functions.py", line 269, in save_analysis
cluster_json = get_clusters(analysis_data, k)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/functions.py", line 283, in get_clusters
X_std, data_df, design_df = get_standardized_df(analysis_data, axis, pk_cols=IDS)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/functions.py", line 303, in get_standardized_df
X_std = inference.standardize_df(inference.data_df, log=True, axis=axis)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/pipelines.py", line 58, in standardize_df
if np.all(data_arr >= 0) and log:
TypeError: '>=' not supported between instances of 'str' and 'int'
Might have something to do with display of data?
Similar to MS2LDA MotifDB, would be nice if users can choose to make their analysis public or private.
While uploading metabolomics data from PiMP or standard format
ArchiveStandard.zip
.
Traceback (most recent call last):
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/exception.py", line 34, in inner
response = get_response(request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 115, in _get_response
response = self.process_exception_by_middleware(e, request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 113, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/views/generic/base.py", line 71, in view
return self.dispatch(request, *args, **kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/views/generic/base.py", line 97, in dispatch
return handler(request, *args, **kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/views/generic/edit.py", line 142, in post
return self.form_valid(form)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/create_analysis_view.py", line 59, in form_valid
species_list, metabolic_pathway_only)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/create_analysis_view.py", line 125, in get_data
results, species_list, current_user, metabolic_pathway_only)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/functions.py", line 234, in save_analysis
user=current_user)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/db/models/manager.py", line 82, in manager_method
return getattr(self.get_queryset(), name)(*args, **kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/db/models/query.py", line 420, in create
obj = self.model(**kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/db/models/base.py", line 501, in __init__
raise TypeError("%s() got an unexpected keyword argument '%s'" % (cls.__name__, kwarg))
TypeError: Analysis() got an unexpected keyword argument 'user'
It's slow
The box plots for metabolites don't show when "Show measurements" is clicked. This happens when only metabolite data is loaded - it does not occur when transcriptomics and metabolomics data are both loaded. Test with ArchiveStandard.zip.
df.ix has been removed from pandas version 1.0, but it's still being used in clustergrammer-py. We should submit a pull request to fix this.
Traceback (most recent call last):
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/exception.py", line 34, in inner
response = get_response(request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 115, in _get_response
response = self.process_exception_by_middleware(e, request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 113, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/views/generic/base.py", line 71, in view
return self.dispatch(request, *args, **kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/views/generic/base.py", line 97, in dispatch
return handler(request, *args, **kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/views/generic/edit.py", line 142, in post
return self.form_valid(form)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/create_analysis_view.py", line 59, in form_valid
species_list, metabolic_pathway_only)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/create_analysis_view.py", line 125, in get_data
results, species_list, current_user, metabolic_pathway_only)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/functions.py", line 269, in save_analysis
cluster_json = get_clusters(analysis_data, k)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/functions.py", line 288, in get_clusters
json_data = to_clustergrammer(X_std, design_df)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/functions.py", line 332, in to_clustergrammer
calc_cat_pval=False, run_enrichr=run_enrichr, enrichrgram=enrichrgram)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/clustergrammer/__init__.py", line 99, in cluster
enrichrgram=enrichrgram)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/clustergrammer/make_clust_fun.py", line 20, in make_clust
df = run_filter.df_filter_col_sum(df, threshold)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/clustergrammer/run_filter.py", line 56, in df_filter_col_sum
df['mat'] = grab_df_subset(df['mat'], inst_rows, inst_cols)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/clustergrammer/run_filter.py", line 74, in grab_df_subset
df = df.ix[keep_rows]
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/pandas/core/generic.py", line 5274, in __getattr__
return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'
After selecting a group, we can create a boxplot, but currently it's too cluttered. Need to improve it.
When loading a selection group, previously selected items are not highlighted correctly.
The query builder in Firdi should support filtering on the pathway table too.
When exporting tables, if the names are truncated and end in ..., then the exported name is incorrect.
When performing a PALS analysis, the following error occurs.
Traceback (most recent call last):
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/exception.py", line 34, in inner
response = get_response(request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 115, in _get_response
response = self.process_exception_by_middleware(e, request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 113, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/inference_view.py", line 522, in inference_pals
pals_df = run_pals(pals_data_source, plage_weight, hg_weight)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/pathway_analysis.py", line 78, in run_pals
pathway_df = pals.get_pathway_df(standardize=False)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/pals/PALS.py", line 51, in get_pathway_df
activity_df = self.get_plage_activity_df(measurement_df, standardize)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/pals/PALS.py", line 82, in get_plage_activity_df
activity_df = self._calculate_pathway_activity_df(measurement_df)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/pals/PALS.py", line 278, in _calculate_pathway_activity_df
activity_df = pd.DataFrame(pathway_activities).set_index([0])
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/pandas/core/frame.py", line 4391, in set_index
raise KeyError("None of {} are in the columns".format(missing))
KeyError: 'None of [0] are in the columns'
[26/Feb/2020 15:02:48] "POST /linker/inference/pals/20 HTTP/1.1" 500 50982811
We are storing the data and other information as serialised strings. This has cascading effects with deletion etc. which mean multiple versions need to kept. This has meant that the database is growing extremely quickly, which probably isn't feasible when more users come on board. Need to replace with proper database schema via django.
Many pathways have significant p-values but they also have very few hits (<=5) on the transcripts/proteins/formula. Other tools usually let user discard these pathways from the results since they're considered unreliable.
Add a new function to let a user share their projects.
The app is quite javascript heavy, but currently we aren't using any js framework.
If we plan to add more features and make the app larger, development progress will become slower since we have to do everything ourselves, boring details like having to remember to update model states when input values change, refreshing HTML in various places to reflect some updated states. We are using MobX which helps with state management, but there's still a lot of manual DOM manipulations going on in various places.
Modern javascript framework takes care of many tedious details and should be used if the app gets more complex. Probably we can use Vue which is easier to integrate to an existing app piecemeal, rather than React that needs us to rewrite everything the react way.
This should be an enhancement in PALS. We can combine e.g. genes + metabolites when doing pathway analysis.
For integration methods, there are two general approaches - tight integration by combining queries in which genes and metabolites are pooled into a single query and used to perform enrichment analysis within their "pooled universe" or loose integration by combining p values in which enrichment analysis is performed separately for genes and metabolites in their "individual universe", and then individual p-values are combined via weighted Z-tests. Moreover, there are three options for computing weights. Let's assume the pathway database contains a total of 100 pathways covering a total of 1000 metabolites and 4000 genes, respectively. Pathway A contains 5 compounds and 45 genes, while pathway B contains 20 compounds and 30 genes.
If Reactome has this info, it could be of use to researchers. How could we incorporate it into the app?
Instead of just 'significant' we should be able to specify the threshold we want to use for filtering in query builder (defaults to 0.05).
It's been noted that people don't understand UniProt ids. Is there a better name we can display on the screen? I know we tried the full names which were way too long, but would something like Gene name work?
Internal Server Error: /linker/get_ensembl_gene_info/25
Traceback (most recent call last):
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/exception.py", line 34, in inner
response = get_response(request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 115, in _get_response
response = self.process_exception_by_middleware(e, request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 113, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/explore_data_view.py", line 97, in get_ensembl_gene_info
display_name = metadata['display_name'] if metadata is not None else ''
KeyError: 'display_name'
[25/Oct/2019 16:20:36] "GET /linker/get_ensembl_gene_info/25?id=YMR120C HTTP/1.1" 500 48904812
/Users/ronan/work/WebOmics/web_omics/linker/views/functions.py:779: FutureWarning:
.ix is deprecated. Please use
.loc for label based indexing or
.iloc for positional indexing
See the documentation here:
http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated
/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/pandas/core/indexing.py:822: FutureWarning:
.ix is deprecated. Please use
.loc for label based indexing or
.iloc for positional indexing
See the documentation here:
http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated
[25/Oct/2019 16:26:31] "GET /linker/get_ensembl_gene_info/25?id=YLR058C HTTP/1.1" 200 816
Internal Server Error: /linker/get_ensembl_gene_info/25
Traceback (most recent call last):
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/exception.py", line 34, in inner
response = get_response(request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 115, in _get_response
response = self.process_exception_by_middleware(e, request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 113, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/explore_data_view.py", line 97, in get_ensembl_gene_info
display_name = metadata['display_name'] if metadata is not None else ''
KeyError: 'display_name'
[25/Oct/2019 16:27:00] "GET /linker/get_ensembl_gene_info/25?id=YBL002W HTTP/1.1" 500 48904817
[25/Oct/2019 16:27:06] "GET /linker/get_ensembl_gene_info/25?id=YMR116C HTTP/1.1" 200 894
Show more decimal points there.
I'm trying to load WebOmics and the python process is taking up ~ 1.3 GB, before any queries have been run. Does this make sense to you?
Probably due to this:
https://github.com/joewandy/WebOmics/blob/master/web_omics/linker/constants.py#L6-L9
Should try to make it so these are loaded only when needed.
It might make an analysis slower to submit. We probbably need to add some kind of progress bar when submitting an analysis (so users don't think it's hanging).
Need to create a static page for landing describing project etc.
rpy2 doesn't install cleanly on a Mac via pipenv. This leads to the following error when starting the app
Exception in thread django-main-thread:
Traceback (most recent call last):
File "/Users/ronan/anaconda3/lib/python3.7/threading.py", line 917, in _bootstrap_inner
self.run()
File "/Users/ronan/anaconda3/lib/python3.7/threading.py", line 865, in run
self._target(*self._args, **self._kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/utils/autoreload.py", line 54, in wrapper
fn(*args, **kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/management/commands/runserver.py", line 117, in inner_run
self.check(display_num_errors=True)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/management/base.py", line 390, in check
include_deployment_checks=include_deployment_checks,
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/management/base.py", line 377, in _run_checks
return checks.run_checks(**kwargs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/checks/registry.py", line 72, in run_checks
new_errors = check(app_configs=app_configs)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/checks/urls.py", line 40, in check_url_namespaces_unique
all_namespaces = _load_all_namespaces(resolver)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/checks/urls.py", line 57, in _load_all_namespaces
url_patterns = getattr(resolver, 'url_patterns', [])
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/utils/functional.py", line 80, in __get__
res = instance.__dict__[self.name] = self.func(instance)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/urls/resolvers.py", line 584, in url_patterns
patterns = getattr(self.urlconf_module, "urlpatterns", self.urlconf_module)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/utils/functional.py", line 80, in __get__
res = instance.__dict__[self.name] = self.func(instance)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/urls/resolvers.py", line 577, in urlconf_module
return import_module(self.urlconf_name)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
File "<frozen importlib._bootstrap>", line 983, in _find_and_load
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 728, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/Users/ronan/work/WebOmics/web_omics/web_omics/urls.py", line 8, in <module>
path('linker/', include('linker.urls')),
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/urls/conf.py", line 34, in include
urlconf_module = import_module(urlconf_module)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
File "<frozen importlib._bootstrap>", line 983, in _find_and_load
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 728, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/Users/ronan/work/WebOmics/web_omics/linker/urls.py", line 3, in <module>
from . import views
File "/Users/ronan/work/WebOmics/web_omics/linker/views/__init__.py", line 1, in <module>
from linker.views.create_analysis_view import *
File "/Users/ronan/work/WebOmics/web_omics/linker/views/create_analysis_view.py", line 12, in <module>
from linker.views.functions import reactome_mapping, save_analysis, change_column_order, get_context
File "/Users/ronan/work/WebOmics/web_omics/linker/views/functions.py", line 22, in <module>
from linker.views.pipelines import WebOmicsInference
File "/Users/ronan/work/WebOmics/web_omics/linker/views/pipelines.py", line 11, in <module>
from rpy2.robjects.packages import importr
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/rpy2/robjects/__init__.py", line 16, in <module>
import rpy2.rinterface as rinterface
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/rpy2/rinterface/__init__.py", line 51, in <module>
from rpy2.rinterface._rinterface import (baseenv,
ImportError: dlopen(/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/rpy2/rinterface/_rinterface.cpython-37m-darwin.so, 2): Library not loaded: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib
Referenced from: /Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/rpy2/rinterface/_rinterface.cpython-37m-darwin.so
Reason: image not found
Due to uncertainty in peak annotation, a single compound can be associated with multiple expression values. In this case, which expression values to send to Reactome? (see commit 834b988).
We could follow PALS Viewer and average the expression values before sending them to Reactome. See glasgowcompbio/PALS@c0cc7ed
When a crop is done on a large number of features, the page hangs and becomes unresponsive. If this is always going to be an issue, we should perhaps limit the crop size.
In the genes heatmap (not sure about others), when we click for cluster information and additional options, a list of genes is given and a piece of text saying send genes to Enrichr. This text doesn't work.
Once a group is created, it would be nice if we can export it, maybe as CSV or dataframes.
User shouldn't be able to create a new group when it's read-only.
Currently we still display the hypergeometric weight when creating a PLAGE analysis. This can be removed.
Got the following error message when trying to run deseq2 on windows. Seems like it's an rpy2 problem.
2019-11-26 11:05:30.751 | WARNING | linker.views.inference_view:inference_deseq_t_test:155 - Failed to run DESeq2: name 'localconverter' is not defined
When a set up genes is selected and Goatools is run, there is no output. The console shows the following
Load GOEA Gene Ontology Analysis ...
fisher module not installed. Falling back on scipy.stats.fisher_exact
0% 0 of 0 population items found in association
Run GOEA Gene Ontology Analysis: current study set of 0 IDs ...
[04/Dec/2019 17:21:15] "POST /linker/get_gene_ontology/14 HTTP/1.1" 200 216
There are definitely genes selected.
[26/Sep/2019 16:08:54] "GET /linker/list_groups/11 HTTP/1.1" 200 12
[26/Sep/2019 16:08:55] "GET /linker/get_heatmap_data/11 HTTP/1.1" 200 3394596
MATCH (dbo:DatabaseObject)-[:summation|:literatureReference]-(ss)
WHERE
dbo.stId = {reactome_id}
RETURN
dbo.stId as reactome_id,
dbo.speciesName as species,
dbo.isInferred as inferred,
ss.displayName as display_name,
ss.text as summary_text,
ss.schemaClass as summary_type,
properties(ss) as summary_props
MATCH (rle:ReactionLikeEvent)-[rr:input|output|catalystActivity
|physicalEntity|regulatedBy|regulator|hasComponent|hasMember
|hasCandidate*]->(dbo:DatabaseObject)
WHERE
rle.stId IN {reaction_ids}
RETURN
rle.stId AS reaction_id,
dbo.stId AS entity_id,
dbo.schemaClass AS schema_class,
dbo.displayName as display_name,
extract(rel IN rr | type(rel)) AS types
[26/Sep/2019 16:09:19] "GET /linker/get_reactome_reaction_info/11?id=R-MMU-1168910 HTTP/1.1" 200 847
Internal Server Error: /linker/get_ensembl_gene_info/11
Traceback (most recent call last):
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/exception.py", line 34, in inner
response = get_response(request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 115, in _get_response
response = self.process_exception_by_middleware(e, request)
File "/Users/ronan/.local/share/virtualenvs/web_omics-VCzYizAw/lib/python3.7/site-packages/django/core/handlers/base.py", line 113, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/Users/ronan/work/WebOmics/web_omics/linker/views/explore_data_view.py", line 97, in get_ensembl_gene_info
display_name = metadata['display_name'] if metadata is not None else ''
TypeError: 'int' object is not subscriptable
The DESeq2 results seem incorrect. The displayed fold change is opposite to the box plots - one of them must be wrong.
Got the following error when running DESeq2:
Error in DESeqDataSet(se, design = design, ignoreRank) :
some values in assay are not integers
(a) Upload of exported peak table from PiMP to WebOmics is broken when the columns InchiKey and Identification are included in the data.
(b) Currently all KEGG annotations for every peak in the uploaded data will be used, regardless of whether they've been identified, annotated with/without fragments. This might not be what we want, and it could affect for example pathway analysis results. Might need to implement some kind of filtering?
A feature request for the http://webgestalt.org/ service to be integrated in some way.
When uploading a standard metabolomics analysis with ChEBI identifiers, the following is seen in the terminal.
2020-02-25 16:54:43.691 | INFO | linker.views.functions:reactome_mapping:35 - Converting kegg ids -> chebi ids
2020-02-25 16:54:43.691 | WARNING | linker.views.functions:reactome_mapping:39 - Not found: 15428
2020-02-25 16:54:43.691 | WARNING | linker.views.functions:reactome_mapping:39 - Not found: 32507
2020-02-25 16:54:43.692 | WARNING | linker.views.functions:reactome_mapping:39 - Not found: 32508
2020-02-25 16:54:43.692 | WARNING | linker.views.functions:reactome_mapping:39 - Not found: 57305
2020-02-25 16:54:43.692 | WARNING | linker.views.functions:reactome_mapping:39 - Not found: 15724
2020-02-25 16:54:43.692 | WARNING | linker.views.functions:reactome_mapping:39 - Not found: No result
2020-02-25 16:54:43.692 | WARNING | linker.views.functions:reactome_mapping:39 - Not found: 5141
2020-02-25 16:54:43.692 | WARNING | linker.views.functions:reactome_mapping:39 - Not found: 30856
2020-02-25 16:54:43.692 | WARNING | linker.views.functions:reactome_mapping:39 - Not found: 51022
etc.
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