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error for phenotype traits
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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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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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