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scripts
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(though there's still a minor issue with a few datasets)
Added some header data to mapping output file
Fixed links in Network Group nodes/edges
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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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* 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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GEMMA mapping accuracy.
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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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and uncommented simplejson import
Added "Reset" option to network graph that returns all the nodes/edges
Made the visualization options area in the network graph a little wider
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settings
Run with
./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
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Also hard-coded the removal of Macaque Monkey since I couldn't think of a good way to retroactively check if every dataset in a species is confidential
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Fixed script that generates dataset dropdown json file to include accession id
Fixed dataset link on search results page
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some corresponding imports
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Currently we still usually get our samplelists from the genofile. This is
dumb because it results in us having a bunch of "dummy" genofiles for certain
data sets (seems to be mostly human ones). This means that checking for the
genofile alone isn't enough to determine if a mapping method should exist
for a given group
I wrote some code that will instead get the samplelist from the plink .fam file
for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy
.geno files, but we can't yet do so because it's currently the only place we seem to be storing
the sample list for some groups.
I also moved gemma into the plink directory to get it out of the git tree.
Since it uses the same files as plink, it doesn't make sense for it
to be in its own separate directory
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Genotype groups when the corresponding data sets do not exist
Interval Mapping no longer shows up for human traits
Fixed the appearance of the mirror links on the main page
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pyLMM is more than 20 (due to speed)
Changed the port in the flask settings to 5002 due to adding the new
production server branch
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Conflicts:
wqflask/wqflask/static/new/javascript/dataset_select_menu.js
wqflask/wqflask/templates/corr_scatter_plot_old.html
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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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adding the correlation matrix page
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Committer: Lei Yan <lei@penguin.uthsc.edu>
On branch master
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