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other functions
Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages
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when loading and more easily control cell contents
Added typeahead to snp_browser (still need to tell it only to use it for rat, though)
Added WebGestalt link to collection page (still need to add it and BNW to other trait list pages)
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results from Chromosome 1
Fixed issue where traits couldn't be added to a collection from the global search results
Made some improvements to the gene global search table
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HTML table, and adding loading text
Made some changes to make trait page SNPs link point to GN2 SNP Browser, as well as make other links open in new tabs/windows
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Changed Variant Browser to display gene name under "Domain" when the user searches a gene term and rows are mislabeled "Intergenic"
Fixed Chr option to display correct chromosomes for different species
Fixed order for correlation drop-down on trait page
Fixed some appearance issues with the mapping results table
Improved appearance of correlation scatterplot page
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Added option to submit traits in collection to BNW
Fixed issue with "x" values for user-submitted traits
Fixed issue where post-publications descriptions were wrongly appearing in global search results
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Updated style for a variety of tables
Moved transform/blocking tools for trait sample table into its own tab
Added some new customization options to network graph
Started work on implementing third party link-outs
Updated drop-down generation script to order datasets according to CreateTime
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Put transform/blocking tools into their own tab (still need to change formatting of tab's contents)
Improved appearance of search result page table (still need to change a few other tables)
Fixed issue that caused parent/f1 strains to not be blocked correctly when using "block by index" tool
Basic Stats figures now load when the user clicks the tab, to improve initial page load time
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inconsistent error
Added change to change maf depending upon number of sample values
Committing in-process changes to how sample table is built on trait page (to make it look better and more compact)
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the same group
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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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Forgot to add to change user to root during the last commit
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Since I know I'll forget otherwise, updated instructions on starting up ES
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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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Gemma optimized for production
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Added "change user to elasticsearch" to the description of how to start elasticsearch
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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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I added the command to start elasticsearch, since I've had to look it up/ask Pjotr about it a couple times now.
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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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