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Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
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with Plotly
GEMMA now has option to select genotypes
Updated dataset select dropdowns to be ordered correctly
Fixed dataset select dropdowns for correlations to not show confidential datasets
Added Skewness and Kurtosis to Basic Statistics table
Fixed Verify and RNA-seq buttons on trait page
Temporarily hardcoded Reference page until we get it to link with database
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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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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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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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Various changes
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(1054, "Unknown column 'mouse' in 'where clause'") [SQL: '\n select Geno)
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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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settings
Run with
./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
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fetch1 to return a tuple
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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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Added data_scale to dataset objects and basic stats table will now check data scale when calculating range
Made interval analyst results table work with datatables
Changed the appearance of the basic stats table some by giving it a border
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[PATCH 039/100] Removing commented code
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[PATCH 038/100] Fix compile errors
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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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Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1)
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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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not work because of the new dataset_menu_structure.json file
An Intro section is also added to the header, though for the time being its contents aren't populated and the edit option isn't working
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pylmm was wrong
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