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for non-mRNA Assay datasets
Increased digits of some Basic Statistics values from 2 to 3
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groups should show dominance effect
Minor changes/improvements for trait page
Updated dataset_menu_structure.json
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GEMMA mapping accuracy.
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method.
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Temporarily removed second sample table for CFW traits
Fixed location of global search bar to work with wider screens
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Various changes/fixes
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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
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tables
Disabled sorting for the first column (check box) of the samples tables
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Various changes
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Updated dataset_menu_structure.json
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loading a collection or doing ctl analysis
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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
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sample p
Set default sort for correlation page to sample p
Improved appearance of correlation matrix some by decreasing line height
Added labels to each figure/table on the correlation page
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(1054, "Unknown column 'mouse' in 'where clause'") [SQL: '\n select Geno)
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which would result in wrong correlation results
Fixed issue where the mean would sometimes be displayed into of the additive effect
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(related to factor loadings table)
Also improved factor loads table to show only two factors when there are two traits
Fixed error related to get_traits_from_collections.js being called in collections/list before jquery is defined
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results pages
Improved the way the table width is set for search results page
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creation from the main CTL analysis code
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cytoscape.js network
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cytoscape.js
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Fixed issue where I forgot to remove a parameter from jsonable_table_row in trait.py
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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
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.geno files.
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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)
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The "Database" part of the metadata isn't displayed for global search table downloads
In both regular and global search, the table can not be sorted by whether the first column is checked
Removed some unused datatables/javascript from the regular and global search page html
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Only checked traits are now downloaded and all traits are downloaded if nothing is checked
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Still need to add metadata and change it to where only selected traits are exported
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Changed formatting of a couple things in search results text (capitalizing/underlining "terms" and bolding the search term)
Changed "Gene" label on trait page to "NCBI" and removed GenBank link
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working right now
Ran some end of line conversion on rqtl_mapping because there were a few ^M's
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a couple functions in collect.py to more accurately reflect when they're called
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