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for mapping
- Now shows error page for Correlation Matrix if traits aren't all from the same group (later need to make it check for shared samples, since different groups may contain some of the same samples
- Mapping results page now displays the genofile in the information section
- Only show Interval Analyst if species is mouse or rat (previously it would show a blank table for other species)
- Network Graph now only shows links in a node's info if the relevant information (for example geneid) exists, and the label changes depending on the type of data set
- Other minor changes to the appearance of the Network Graph menu (less white space, plus clickable descriptions for a couple options)
- Improved Correlations Results page to shorten Description and Authors cell content for Phenotype traits (to keep table width manageable)
- Changed the glossary links for LRS and Additive Effect columns for Gene Global Search
- Improved appearance for Phenotype Global Search results
- Temporarily removed Mapping options/features that don't work from the trait page
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appearance for mRNA assay data sets (still need to improve it for others)
Fixed minor logic issue in trait.py
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Graph interface
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* refactored ./bin/genenetwork2 and /etc/default_settings
- better detection of Guix
- removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS
- removing some default settings, such as PYLMM_COMMAND
- rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY
- added GUIX_JS_PATH for JS modules
* Added documentation on installing binary GN2
* Updated Twitter board to latest version in Guix - it had broken
* Updated many tools in the latest Guix profile
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Updated dataset menu dropdown info
Began adding option to download statistics figures as PNG
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different from base dataset
Improved collection list and view table appearances
Added question mark image for glossary entries in table headers
Fixed issue where extra decimal place sometimes appeared in bar chart Y axis tick values
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Improved appearance of search result and collection tables
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- 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
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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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