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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
2013-11-27Clicking a trait in "color by trait" now gets all of its sample valuesZachary Sloan
that will be used to color the bar graph
2013-11-26Made some progress towards getting the traits inside a collection to display ↵Zachary Sloan
on hover
2013-11-25Got the interval mapping results into a tableZachary Sloan
2013-11-01Merge /home/sam/geneZachary Sloan
2013-10-30More work on collectionsSam
2013-10-25Began working on color coding bar chart by extra attributesZachary Sloan
2013-09-13Merge https://github.com/zsloan/genenetworkLei Yan
Resolved conflicts: wqflask/base/trait.py wqflask/wqflask/correlation/correlationFunction.py wqflask/wqflask/correlation/correlation_function.py wqflask/wqflask/correlation/correlation_functions.py wqflask/wqflask/correlation/show_corr_results.py
2013-08-07Fixed things with the dataset dropdowns and mRNA datasetsZachary Sloan
Improved the templates for a couple pages related to changing user password, etc
2013-07-18Added Amelie's rat data genotypesZachary Sloan
Got human mapping mostly working Fixed dataset dropdown menus
2013-07-16Wrote code that can get a dataset's type for every single GNZachary Sloan
dataset; previously we could not view traits in datasets that were not in the DBType table in the database
2013-06-25Merge git://github.com/zsloan/genenetwork into flaskLei Yan
2013-06-20Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flaskZachary Sloan
Conflicts: wqflask/requirements.txt wqflask/wqflask/correlation/show_corr_results.py
2013-06-19Moved the normalize_values function to separate file corr_result_helpers.pyLei Yan
Added docstring test to normalize_values Number of overlapping samples column now displays correctly in the correlation results page
2013-06-19Fixed issue where the Mean Expr, Max LRS, and Max LRS Location columnsLei Yan
in the correlation page weren't displaying
2013-06-19Merge branch 'flask' of git://github.com/zsloan/genenetwork into flaskLei Yan
Conflicts: wqflask/base/data_set.py
2013-06-19Changed QTL parameter name to "get_qtl_info" on trait.py andLei Yan
other places it's called, like search_results.py Added other trait info fields to correlation results page
2013-06-19Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flaskZachary Sloan
Conflicts: wqflask/base/data_set.py wqflask/wqflask/views.py Fixed a couple conflicts to merge Lei's code related to the correlation page
2013-06-13Fixed issue where too much memory was used as a result of creating aLei Yan
dataset object for each trait in the correlation results Added new fields/columns for each trait in the correlation result table (max LRS, max LRS location, mean expression) Fixed error if trait doesn't have these fields
2013-06-11Put trait info for correlation results page into a dictionary insteadLei Yan
of storing list of GeneralTrait objects Added print statements to track memory usage
2013-05-31Fixed the location column for the quick search pageZachary Sloan
Began writing some jquery to automatically open the first tab within each species tab on the quick search page (not done yet)
2013-05-30Rewrote some code in get_trait_info in dataset.pyLei Yan
Added spearman correlation to show_corr_results and template
2013-05-08Worked on correlation pageLei Yan
Wrote function in dataset.py that gets all the traits in a dataset and their sample values
2013-01-18Renamed CorrelationPage.py to show_corr_results.pyZachary Sloan
Worked with correlation code; got to the code that begins to do the actual correlations Created a function "get_dataset_and_trait" in the new file "helper_functions.py" because the code initializing the dataset and trait objects was repeated in multiple places
2013-01-03Created template for marek regression page and made the compute button directZachary Sloan
to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py
2012-12-07Got basic statistics in show_trait to display the correct numberZachary Sloan
of samples for each group Got show_trait page to display for genotype traits
2012-12-06Made many small changes to show_trait/data_set/search_results/trait toZachary Sloan
remove use of the formData object and cursor
2012-12-05Renamed webqtlTrait.py to trait.pyZachary Sloan
Renamed webqtlTrait class to GeneralTrait Began process of removing fd from show_trait.py Created DatasetGroup object in data_set.py (this may end up becoming its own file later if it becomes big enough)
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