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using precomputed kinship matrix
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drawing SNP density chart when results exceed a certain value, plus a couple minor fixes
Changed the header bar to put a few items under the "Help" option, since previously the header was too long and would go to a second line when the browser window width was smaller
Changed dataset info link on trait page to same as one on search page
Changed the mapping default to non-LOCO for the time being, until it is faster
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chart if results exceed some number (5000 on GN1)
- Removed unnecessary options from the mode bar for the trait page Plotly figures and changed the default to highlight points the mouse is hovering over
- Changed some file/function names related to mapping, which previously were erroneously named "marker_regression"
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reference to probeSetSearch wasn't removed
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- Added all current SNP browser code (not complete yet)
- Added change to convert_geno_to_bimbam that makes it ignore .geno files marked as "filler" (so ones where the .geno file is fake and we sometimes directly receive the genotypes as BIMBAM)
- Changes TheSpecies object in species.py to accept species name as well as dataset name
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just clicking their row in collection
- Cofactor color picker now works in Safari/Macs
- Displays N for relevant samples in trait page sample table
- Don't show bar chart when N>256
- Mapping loading page contents better centered
- Anonymous collections timeout correctly listed as 30 days now
- Minor allele frequency can actually be changed for GEMMA now (previously didn't work)
- Fixed transcript position marker location for mapping results
- Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password
- Users can now map with submitted traits
- Histogram width changes depending upon number of bins (need to improve this still)
- Improved Q-q plot (previously called "probability plot")
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Added Phenogen track to mapping results
Added comparison bar chart figure
Simplified global search to not build trait/dataset objects, which speeds thing up considerably
Fixed correlation matrix to correctly deal with 0 values
Fixed issue where anonymous collections couldn't be created if none already existed
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Figures now correctly rescale when transforms are applied
Fixed height of probability plot
Removed some text related to pylmm since it's currently not being used
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trait page
Got figures mostly working with transformed values, except for changing the y-axis range of one
Fixed issue with the home page "Make Default" button position (as well as the drop-downs in general)
Added timeout to Elasticsearch connection to fix related error
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previously
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should have their full functionality back (adding/removing collections, adding/removing traits, etc)
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staging, though still not sure why it's working on production without that change
Added script to convert the dryad format genotype files to BIMBAM
removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable
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sample data into ElasticSearch
Added option to replace trait page sample/strain values with normalized ones
Began editing Lei's scatterplot code
Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)
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Fixed issue where GEMMA + LOCO wasn't working with AIL (and probably some other groups)
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instead of -lmm 1 (Wald test)
Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)
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set width
Changed to using BIMBAM files to build Marker objects in dataset.py
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some problem. Probably better to leave this file alone for the time being.
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Removed some unused code from the other files listed
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marker_regression_gn1.py
marker_regression.py
do_search.py
export_traits.py
heatmap.py
GeneUtil.py
heatmap.html
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testing
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* I can't swear on this, but it seems the presence of these statements
was causing elasticsearch to act weird.
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* Update the indexes mappings to be compatible with the newer
Elasticsearch 6.2.* series.
Close the index before updating it, and reopen it after to help with
the re-indexing of the data.
* Update the error logger to include the exception that was thrown.
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* Prevent elasticsearch from analysing and tokenising the email_address
field so as to avoid issue with getting back all email addresses with
the same domain as the one being searched for.
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* Ensure the return is at the correct indentation level so that it is
executed correctly.
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* Ensure that the user actually provides an email address when they try
to use the forgot password feature.
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missing before
Removed a bunch of unused coded from all correlation-related files and the ctl analysis code
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the remaining could should be migrated to the files that use them at some point.
Some of this code was in the correlation code but not being used, so it wss removed from there as well.
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pretty sure also isn't used any more.
Also removed some other unused code from the files listed
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variable not being initialized
Removed a bunch of unused statistical functions from Plot.py and webqtlUtil.py. I figure that if we ever need them again, there's probably some third party library that includes them.
Also removed unused file AJAX_table.py and other unused code from several other files
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scripts
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being used except corestats, which I moved to utility
Removed box plot code from Plot.py since we no longer use it either
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