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path: root/wqflask/utility/Plot.py
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2023-12-29Namespace all modules under gn2.Arun Isaac
We move all modules under a gn2 directory. This is important for "correct" packaging and deployment as a Guix service.
2022-08-31Remove usage of "logger" and un-necessary comments wrt the sameMunyoki Kilyungi
Logging is used to introspect variables or notify the commencement of a given operation. Logging should only be used to log errors. Also, most of the logging is either "logger.debug" or "logger.info"; and this won't show up in production/testing since we need a logging level above "WARNING" for them to show up. * wqflask/base/data_set.py (create_datasets_list): Remove logger. (Markers.add_pvalues): Ditto. (DataSet.retrieve_other_names): Ditto. * wqflask/base/mrna_assay_tissue_data.py: Ditto. * wqflask/base/webqtlCaseData.py: Ditto. * wqflask/db/call.py (fetch1): Ditto. (gn_server): Ditto. * wqflask/db/gn_server.py: Ditto. * wqflask/maintenance/set_resource_defaults.py: Ditto. * wqflask/utility/Plot.py (find_outliers): Ditto. * wqflask/utility/gen_geno_ob.py: Ditto. * wqflask/utility/helper_functions.py: Ditto. * wqflask/utility/pillow_utils.py: Ditto. * wqflask/utility/redis_tools.py: Ditto. * wqflask/wqflask/api/gen_menu.py (get_groups): Ditto. * wqflask/wqflask/api/mapping.py: Ditto. * wqflask/wqflask/api/router.py (get_dataset_info): Ditto. * wqflask/wqflask/collect.py (report_change): Ditto. * wqflask/wqflask/correlation/corr_scatter_plot.py: Ditto. * wqflask/wqflask/ctl/ctl_analysis.py (CTL): Ditto. (CTL.__init__): Ditto. (CTL.run_analysis): Ditto. (CTL.process_results): Ditto. * wqflask/wqflask/db_info.py: Ditto. * wqflask/wqflask/do_search.py (DoSearch.execute): Ditto. (DoSearch.mescape): Ditto. (DoSearch.get_search): Ditto. (MrnaAssaySearch.run_combined): Ditto. (MrnaAssaySearch.run): Ditto. (PhenotypeSearch.run_combined): Ditto. (GenotypeSearch.get_where_clause): Ditto. (LrsSearch.get_where_clause): Ditto. (MeanSearch.run): Ditto. (RangeSearch.get_where_clause): Ditto. (PvalueSearch.run): Ditto. * wqflask/wqflask/docs.py: Ditto. * wqflask/wqflask/export_traits.py: Ditto. * wqflask/wqflask/external_tools/send_to_bnw.py: Ditto. * wqflask/wqflask/external_tools/send_to_geneweaver.py: Ditto. * wqflask/wqflask/external_tools/send_to_webgestalt.py: Ditto. * wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto. * wqflask/wqflask/heatmap/heatmap.py: Ditto. * wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults): Ditto. * wqflask/wqflask/marker_regression/gemma_mapping.py: Ditto. * wqflask/wqflask/marker_regression/plink_mapping.py (run_plink): Ditto. * wqflask/wqflask/marker_regression/qtlreaper_mapping.py (run_reaper): Ditto. * wqflask/wqflask/marker_regression/rqtl_mapping.py: Ditto. * wqflask/wqflask/marker_regression/run_mapping.py (RunMapping.__init__): Ditto. * wqflask/wqflask/parser.py (parse): Ditto. * wqflask/wqflask/search_results.py (SearchResultPage.__init__): Ditto. * wqflask/wqflask/update_search_results.py (GSearch.__init__): Ditto. * wqflask/wqflask/user_login.py (send_email): Ditto. (logout): Ditto. (forgot_password_submit): Ditto. (password_reset): Ditto. (password_reset_step2): Ditto. (register): Ditto. * wqflask/wqflask/user_session.py (create_signed_cookie): Ditto.
2021-08-23Account for situations where the minimum permutation value is also above ↵zsloan
webqtlConfig.MAXLRS; previously threw an error
2021-04-30autopep8: Run autopep8 100 times with target rulesBonfaceKilz
Rules used are: E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242, E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306, E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121, E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
2021-04-30autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133BonfaceKilz
2021-04-30autopep8: Fix E101, E11BonfaceKilz
2021-04-30autopep8: Fix E70 and E701BonfaceKilz
2021-04-30autopep8: Fix E501BonfaceKilz
2021-04-30autopep8: Fix E301,E302,E303,E304,E305,E306BonfaceKilz
2021-04-30autopep8: Fix E20-E27BonfaceKilz
Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3
2020-08-26Remove "from __future__ import new_feature" statementsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
2020-08-26Update corestats importBonfaceKilz
* wqflask/utility/Plot.py: import corestats from the utility module.
2020-08-26Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-08-24Remove unused importsBonfaceKilz
* wqflask/utility/Plot.py: Remove unused imports like "numarray". "numarray" is does not have py3 support so it's important to remove references to it.
2020-08-19Remove extra whitespace(or add it) from comma separated itemsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19Rename xrange() to range() and wrap existing range() calls with listBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-xrange>
2020-08-18Fix malformed docstringBonfaceKilz
* wqflask/utility/Plot.py: Update docstring.
2020-08-08Use draw_rotated_text()Muriithi Frederick Muriuki
Use the new draw_rotated_text() function to draw the text rotated as was formerly done. * wqflask/utility/Plot.py (plotBar): Use draw_rotated_text(). * wqflask/wqflask/marker_regression/display_mapping_results.py: (DisplayMappingResults) Use draw_rotated_text().
2020-08-08Fix font pathsMuriithi Frederick Muriuki
* wqflask/utility/Plot.py: Update font paths. * wqflask/fonts/ttf: Update font files.
2020-08-08Migrate code from Piddle to PillowMuriithi Frederick Muriuki
* wqflask/wqflask/marker_regression/display_mapping_results.py: Add font files (DisplayMappingResults): Update the code from the Piddle way of things to the Pillow way of things, for example, replace: - pid.drawRect(...) with im_drawer.rectangle(...) - pid.drawString(...) with im_drawer.text(...) - pid.drawPolygon(...) with im_drawer.polygon(...) etc. * wqflask/utility/Plot.py: Migrate code from the older, unsupported Piddle to the newer Pillow library.
2020-07-08Removed remaining unused references to the old qtlreaperzsloan
2019-02-22Fixed some appearance issues with several tableszsloan
Fixed issue where cofactor selection screens were broken Changed case attributes to be applied across groups, though need to discuss this with Rob since it shouldn't always be done this way Added new inversion transformation
2018-04-09Removed svg.py, which I know isn't used, and webqtlFormData, which I'm ↵zsloan
pretty sure also isn't used any more. Also removed some other unused code from the files listed
2018-04-09Fixed issue that caused and error for certain types of mapping due to ↵zsloan
variable not being initialized Removed a bunch of unused statistical functions from Plot.py and webqtlUtil.py. I figure that if we ever need them again, there's probably some third party library that includes them. Also removed unused file AJAX_table.py and other unused code from several other files
2018-04-09Removed the basicStatistics directory/contents because nothing there was ↵zsloan
being used except corestats, which I moved to utility Removed box plot code from Plot.py since we no longer use it either
2016-06-21log: replace print statementsPjotr Prins
2016-06-18Logging: behavioursPjotr Prins
2016-06-18Disable setting sys.pathsPjotr Prins
2016-06-17Removed trailing spaces in .py and .js filesPjotr Prins
2016-04-07SNP Track option should now work for GN1 mapping figurezsloan
Fixed typo in show_trait html that caused the p-value slider to not work for correlations
2016-04-06Permutations (suggestive/significant lines, legend, and histogram) should ↵zsloan
now work for both R/qtl and qtl reaper mapping. Changed the logic for receiving permutation/bootstrap info when loading mapping page in different ways (from show_trait, from remapping, from clicking single chromosome) Added text below figure when Allele Effects selected/relevant
2012-08-29Fixed so that outliers are now correctly highlightedZachary Sloan
2012-06-22Working my way through getting the review and edit data dynamically ↵Sam Ockman
generated in Jinja2
2012-06-05Ran reindent.py recursively on wqflask directorySam Ockman
2012-06-02Coming along in trying to get trait page workingSam Ockman
2012-05-24Trying to get stuff working under new structureSam Ockman
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