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path: root/wqflask/base/trait.py
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2018-10-01- Can now remove cofactors from correlation scatterplot and select them by ↵zsloan
just clicking their row in collection - Cofactor color picker now works in Safari/Macs - Displays N for relevant samples in trait page sample table - Don't show bar chart when N>256 - Mapping loading page contents better centered - Anonymous collections timeout correctly listed as 30 days now - Minor allele frequency can actually be changed for GEMMA now (previously didn't work) - Fixed transcript position marker location for mapping results - Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password - Users can now map with submitted traits - Histogram width changes depending upon number of bins (need to improve this still) - Improved Q-q plot (previously called "probability plot")
2018-08-14Added cofactors to correlation scatterplot and changed it to use Plotlyzsloan
Added Phenogen track to mapping results Added comparison bar chart figure Simplified global search to not build trait/dataset objects, which speeds thing up considerably Fixed correlation matrix to correctly deal with 0 values Fixed issue where anonymous collections couldn't be created if none already existed
2018-04-06Mapping figure output now gives more accurate informationzsloan
Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
2017-06-12Fixed issue where 0.0 values would be converted into X's on the trait pagezsloan
2017-05-31Added various tool options to correlation results page and improved table ↵zsloan
appearance for mRNA assay data sets (still need to improve it for others) Fixed minor logic issue in trait.py
2017-04-05- Temporary traits can be created, viewed, and added to collectionszsloan
- Correct PCA trait data is created but can't be saved yet - Added inner margins by increasing xDomain and yDomain of probability plot on trait page - Increased X/Y-axis label font size - Turned "processes" to 0 on runserver.py for PROD setting, since it doesn't work with threading - Improved appearance of correlation page table - Added links to github to index page - Removed js_data from GEMMA/PLINK mapping results, since it isn't used for those - Removed "Tissue" from trait page for phenotype traits
2017-01-26GEMMA now works with CFW data (had to update where it looks for the input ↵zsloan
files and how it writes the phenotype file) Y-axis for GEMMA now says -log(p) Updated the style of the trait sample data table in the trait page Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs) Updated dataset menu json file Added option to show and hide columns to regular search page using colVis Changed regular and global search result table styles/column widths Began work on user trait submission code (not working yet though) Began work on static loading page for mapping results
2016-12-13Fixed a problem related to the last commit that caused a problem when ↵zsloan
loading a collection or doing ctl analysis
2016-12-12Moved a bunch of functions out of the GeneralTrait class that didn't need to ↵zsloan
be there and changed the code that calls them accordingly Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static) Removed some unused code from show_trait.py changed appearance of table headers some, though needs a little more work Updated dataset_menu_structure.json
2016-11-15Fixed issue where sample values of 0 would sometimes be displayed as 'x', ↵zsloan
which would result in wrong correlation results Fixed issue where the mean would sometimes be displayed into of the additive effect
2016-11-11Fixed problem that caused checkboxes to not work with Scroller search ↵zsloan
results pages Improved the way the table width is set for search results page
2016-11-02Added toggleable short and long labels to correlation matrixzsloan
Fixed issue where I forgot to remove a parameter from jsonable_table_row in trait.py
2016-11-02Added Scroller functionality to regular (but not global) search, which ↵zsloan
increases table load speed In order to implement Scroller (and make table look nicer), all rows are the same height and excess description/authors text is shown in a tooltip Increased table width for non-Geno DBs Fixed issue where Genotype traits did not fetch their location_repr (text for displaying location), causing that column to be blank in searches Fixed issue causing Correlation Matrix cells to not be colored corresponding with their correlation and also increased cell font a little Fixed issue where dataset link in the Correlation Page did not correctly point to corresponding GN1 page
2016-10-25Just removed some extraneous spaces in trait.pyzsloan
2016-10-25Replaced the Download Table button for collection page with python version ↵zsloan
that displays metadata, etc Removed currently unused javascript and css imports related to the DataTables buttons import (since it was replaced with the python export) from regular search, both global searches, and the view_collection page Added a bunch of parameters to the jsonable function for the GeneralTrait object in order to later create a json version of the search results and implement the client-side Scroller feature (which dynamically loads table rows from json when you scroll)
2016-09-29Fix global search "il6" for "Internal Server Error". Add single quotes into ↵Lei Yan
MySQL query.
2016-08-24Replaced post-publication description with pre-publication description for ↵zsloan
confidential phenotype traits in search results and trait pages Fixed table style for mapping results and interval analyst tables and added additive/dominance effect columns to the former Fixed mapping figure X-axis to accurately label Centimorgans vs Megabases (previously it would always say Megabases) Removed the "Sequence Site" marker from mapping result figure when mapping with genetics (centimorgans) scale Removed some unused javascript libary imports from search/global search pages
2016-08-16Users can now select specific traits from collection when using collection ↵zsloan
tools (correlation matrix, wgcna, etc) To do the above, changed the way form submission worked for those features; previously each feature had its own form, but that was dumb so instead I wrote a javascript function that just changed a single form's target url Duplicate traits can no longer by added to collections Fixed the digits for a few table columns in collection (additive effect, etc).
2016-06-26Resolve conflictsPjotr Prins
2016-06-24Removed function 'get_info' in trait.py that was never used and reomved ↵zsloan
'get_trait_info' call from search_result_page.py because its query was already being run
2016-06-23Logger: SQLPjotr Prins
2016-06-23Logger: SQLPjotr Prins
2016-06-23Refactored dir name dbFunction to dbPjotr Prins
2016-06-17Removed trailing spaces in .py and .js filesPjotr Prins
2016-06-03Changed appearance of tables to more easily differentiate them from the rest ↵zsloan
of the page (still not totally pleased with them though) Fixed issue where some N/A lrs scores and additive effects were being changed to 0's, which was misleading and kept them from always being sorted at the bottom. They now appear as N/A.
2016-05-31Fixed error when MrnaAssay search results didn't have a geneidzsloan
2016-05-26Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-05-26Issue with certain samples (like BXD65a, ones were there are multiple for a ↵zsloan
single BXD or whatever) should be fixed for different mapping methods and data set types Renamed directories with genotypes so tools.py didn't need to be changed (which might mess up other deployments) Fixed error when searching genotype data sets
2016-05-23Reaper mapping results are now correct and account for samples with two ↵zsloan
names (like BXD65a) R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.
2016-05-18Updated dataset selection dropdown menus and fixed error caused by traits ↵zsloan
with no description
2016-04-19Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
Conflicts: wqflask/base/trait.py
2016-04-13Moved the code getting the description/location because it was throwing an ↵zsloan
error for phenotype traits
2016-04-13Global search should be able to return description and location columns nowzsloan
2016-04-11Figured out how to load results into dataTable using AJAX, but still need to ↵zsloan
get it working with Scroller correctly Added code getting the description, etc to trait.py since it was missed from last commit
2016-04-11Changed the way trait data is retrieved for the global search page (it now ↵zsloan
gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py) This change increases the speed by a bit (85 seconds to 66 seconds for example) Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
2016-03-18Replaced header with other information in qtl mapzsloan
Began adding menu to qtl map Fixed global search to not retrieve samples (to increase speed) Got the vector plot working again so it can be displayed alongside the gn1-style plot Only display the vector plot when doing GEMMA to speed up (this might not be necessary)
2016-03-14Changed the way headers look across all pageszsloan
Changed the way details are displayed in show trait page Changed search query so that it orders results by symbol
2016-03-02Increased gsearch speed by removing unnecessary query for sample datazsloan
Still slower than preferable due to having to query the gn1 database for every trait in the search results
2015-07-09Some phenotype searches were throwing an error due to an assert statement in ↵zsloan
trait.py. Since I couldn't find the purpose of the assert statement I removed it.
2015-06-29Merge pull request #72 from lomereiter/issue69zsloan
Fixes #69
2015-06-22fixed a few potential security issuesArtem Tarasov
2015-06-18fix all_samples_orderedArtem Tarasov
move duplicated code into a method, handle the case of missing f1/f12 correctly
2015-05-22Fixed issue where correlation didn't work for human traits (and probably ↵zsloan
some others)
2015-05-12Fix #35Artem Tarasov
* 'aliases' and 'location' are shown only where relevant * descriptions for phenotype datasets are provided at the top
2015-04-10Added git large file system (the .gitattributes files) and fixed an issue ↵zsloan
where rat trait pages wouldn't work
2014-12-12Added a additive effect column to search result and collection tablesZachary Sloan
Fixed the header so that it looks fine when resizing
2014-10-02Fixed an error when there's no locus for mRNA expression traitsZachary Sloan
2014-08-21Committer: Lei Yan <lei@penguin.uthsc.edu>Lei Yan
On branch master
2014-06-25Added Karl's correlation matrix codeZachary Sloan
Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
2014-06-06Implimented Karl Broman's lodchart code for the interval mapping function.Zachary Sloan
Suggestive/significant bars and additive effect curve added