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2015-07-01Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
2015-07-01cis and trans LRS searches now work. Still need to get them working in ↵zsloan
combined searches
2015-06-29Merge pull request #72 from lomereiter/issue69zsloan
Fixes #69
2015-06-29Merge pull request #77 from lomereiter/fix_sqlzsloan
SQL security fixes
2015-06-26Fixed minor bug where the static loading bar would remain after the mapping ↵zsloan
results were displayed.
2015-06-26Fixed bug where mapping results sometimes wouldn't display. This would occurzsloan
due to a chromosome (in this case the last) not having any markers. Improved the way plink gets its path/command to use a method similar to the one Pjotr used with pylmm. I'll also do this for the other mapping methods. Fixed issue where the Y axis would always say LOD score. It now says LRS for mapping methods that return LRS Switched interval mapping (qtl reaper) to use the marker_regression template and removed the interval_mapping template (since it's unnecessary) Some commented out changes remain (in show_trait_mapping_tools and create_lodchart) from when I was attempting to open the mapping results in a new page. I had resolved every issue but the mapping javascript (lod_chart) not being able to access js_data (which has all the result data; markers, p-values, etc). I'm pretty sure that this is because js_data was inserted into the html after the page was loaded while the chart code ran immediately. I experimented with adding a short timeout to the mapping javascript and data table javascript, but while it worked for the table it did not work for the mapping figure. I don't know why this is.
2015-06-22Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
Conflicts: wqflask/wqflask/templates/marker_regression.html
2015-06-22Just a few minor changes before pulling Artem's fix to the mapping issue.zsloan
2015-06-22Merge pull request #75 from lomereiter/fix_searchzsloan
fix genotype search
2015-06-22escape docs queryArtem Tarasov
2015-06-22fixed a few potential security issuesArtem Tarasov
2015-06-21fix mapping results loadingArtem Tarasov
2015-06-20fix genotype searchArtem Tarasov
2015-06-18Fixed issue that prevented multiple mapping submissions without refreshing. ↵zsloan
Also changed to where results open in new window instead of colorbox, though an issue remains where the css doesn't seem to be getting imported properly.
2015-06-18removed unused functionArtem Tarasov
2015-06-18fix all_samples_orderedArtem Tarasov
move duplicated code into a method, handle the case of missing f1/f12 correctly
2015-06-18add missing line to webqtlUtilArtem Tarasov
2015-06-17Now you can expand/contract tabs on the trait page by click anywhere on the barzsloan
2015-06-16Finished adding all the extra tools/links below the trait detailszsloan
2015-06-05Added back in some of the options on the trait page; Add, Find, and Verify ↵zsloan
now work. I'll get the other 4 working next.
2015-06-04Fixed a minor issue that was causing position search to not work.zsloan
2015-06-02Wildcards can now be appended to mRNA assay searches, but isn't working ↵zsloan
correctly yet with phenotypes
2015-06-02Added Panduka's Genotation tool link to the trait page, along with the Gene, ↵zsloan
OMIM, and GenBank links
2015-06-02Wildcard search should now work for Genotype searcheszsloan
2015-06-02Wildcard search (*) works for regular mRNA assay and phenotype searches and ↵zsloan
fixed issue with black columns in correlation page
2015-05-26Merge pull request #60 from lomereiter/ppzsloan
add missing file
2015-05-26add missing fileArtem Tarasov
2015-05-26Merge pull request #58 from lomereiter/ppzsloan
Use NVD3 for bar chart and probability plot
2015-05-26fix terminologyArtem Tarasov
2015-05-26use NVD3 for bar chartsArtem Tarasov
added informative tooltips and error bars
2015-05-23pp group selectionArtem Tarasov
2015-05-23fix group selection in blocking by indexArtem Tarasov
2015-05-23Fix trait groupingArtem Tarasov
2015-05-23new probability plot (using NVD3 library)Artem Tarasov
* z scores are computed on the client side (using jStat library) * added Shapiro-Wilk test results
2015-05-22Fixed issue where correlation didn't work for human traits (and probably ↵zsloan
some others)
2015-05-21Changed the digits for additive effect and megabases in the search results tablezsloan
2015-05-20Merge pull request #53 from lomereiter/bar_chart_improvementszsloan
Bar chart improvements
2015-05-20revert database.py setupArtem Tarasov
2015-05-20bar charts polishedArtem Tarasov
* fixed bar chart width (two bars were invisible) * disabled basic stats update effects, if they are not visible * fix: unchecked samples were shown in charts (because attr('checked') was used instead of prop('checked')) * bar chart gets redrawn after checkbox changes * edit_data_change is also called when clicking buttons from the 'Block samples' panel * better bar chart transitions (use sample name as d3 key function)
2015-05-19Fixed an issue causing position search to not work in a combined search.zsloan
2015-05-19Fixed an issue that caused combined search to not workzsloan
2015-05-20improved legendArtem Tarasov
Now the legend is always positioned on top, so that no overlapping with the plot occurs and it's always visible. The legend is now composed of spans, not an SVG anymore. Also increased the legend font size to 20px.
2015-05-19Regular LRS searches and p-value searches now work.zsloan
2015-05-18fix attribute coloringArtem Tarasov
also I found out that there are two legends shown simultaneously, but one is suitable only for discrete values, and the other for continuous; now only the suitable one is shown
2015-05-18Merge branch 'upstream' of github.com:lomereiter/genenetwork2 into issue28Artem Tarasov
2015-05-18fix broken trait pageArtem Tarasov
2015-05-15Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
2015-05-15Position search now works for mRNA assay and genotype data setszsloan
2015-05-15reduce number of queriesArtem Tarasov
2015-05-15wipArtem Tarasov