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Merge from the diet branch
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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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renamed: gn2_lei.conf -> gn2-lei.conf
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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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Add meta info (X axis, Y axis) for Correlation Scatterplot
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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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A couple minor commits
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for non-mRNA Assay datasets
Increased digits of some Basic Statistics values from 2 to 3
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Added genetic_type to DatasetGroup object to differentiate between wh…
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groups should show dominance effect
Minor changes/improvements for trait page
Updated dataset_menu_structure.json
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Changed the way .fam files are written/read, which fixes the issue wi…
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GEMMA mapping accuracy.
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Mapping results figure now correctly says whether GEMMA was used as m…
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method.
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Removed reference to trait_submission since it isn't used yet
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Various changes
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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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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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Thanks. Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalErro…
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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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