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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
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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.
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with no description
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Conflicts:
wqflask/base/trait.py
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error for phenotype traits
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get it working with Scroller correctly
Added code getting the description, etc to trait.py since it was missed from last commit
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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
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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)
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Changed the way details are displayed in show trait page
Changed search query so that it orders results by symbol
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Still slower than preferable due to having to query the gn1 database for every trait in the search results
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trait.py. Since I couldn't find the purpose of the assert statement I removed it.
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Fixes #69
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move duplicated code into a method,
handle the case of missing f1/f12 correctly
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some others)
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* 'aliases' and 'location' are shown only where relevant
* descriptions for phenotype datasets are provided at the top
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where rat trait pages wouldn't work
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Fixed the header so that it looks fine when resizing
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On branch master
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Improved the "scatterplot matrix" feature on the trait page so that
it matches the chosen trait against every selected trait
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Suggestive/significant bars and additive effect curve added
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that will be used to color the bar graph
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on hover
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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
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Improved the templates for a couple pages related to changing user
password, etc
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Got human mapping mostly working
Fixed dataset dropdown menus
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dataset; previously we could not view traits in datasets that
were not in the DBType table in the database
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Conflicts:
wqflask/requirements.txt
wqflask/wqflask/correlation/show_corr_results.py
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Added docstring test to normalize_values
Number of overlapping samples column now displays correctly in the
correlation results page
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in the correlation page weren't displaying
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Conflicts:
wqflask/base/data_set.py
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other places it's called, like search_results.py
Added other trait info fields to correlation results page
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Conflicts:
wqflask/base/data_set.py
wqflask/wqflask/views.py
Fixed a couple conflicts to merge Lei's code related to the correlation page
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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
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of storing list of GeneralTrait objects
Added print statements to track memory usage
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Began writing some jquery to automatically open the first tab
within each species tab on the quick search page (not done yet)
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Added spearman correlation to show_corr_results and template
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Wrote function in dataset.py that gets all the traits in a dataset
and their sample values
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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
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to it
added asbolute_import in data_set.py and trait.py
Made several minor changes and deleted commented out code in trait.py
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of samples for each group
Got show_trait page to display for genotype traits
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remove use of the formData object and cursor
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