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[PATCH 039/100] Removing commented code
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[PATCH 038/100] Fix compile errors
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error for phenotype traits
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gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py)
This change increases the speed by a bit (85 seconds to 66 seconds for example)
Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
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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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Changed the way details are displayed in show trait page
Changed search query so that it orders results by symbol
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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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draw to different chr areas though
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Scatterplot matrix feature only appears if user is logged in now
Committing current progress on mapping page (it can at least import the file now, but there are still errors)
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pylmm was wrong
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Committer: Lei Yan <lei@penguin.uthsc.edu>
On branch master
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phenotype)
Fixed issue where LRS and LOD are sometimes labeled incorrectly
Changed the header of the trait page
Added link to GN1 in header
Fixxed an issue that made permutations not work with pylmm
Fixed "sign in" button when creating a collection while not logged in
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Made changes to the tables of correlation results, collections, and search results:
- Added resizeable columns to correlation results and collections, but not to search results
because it seems that it requires Y scrolling to be set (I'll check if it makes sense to add scrolling
to the search results)
- Correlation results and collections are now in scrolling tables
- The style is the same across all of these tables now
Remaining issues:
- It doesn't seem like I can set the column width when initializing dataTables in
correlation results. I don't know why this is; it might be due to the table already being the size
of a full page. I want to be able to default to some good widths, even if the user can resize them
- I tried adding hoverForMore, but it doesn't seem to cooperate with datatable cells; I think this is
due to having to put the text in a div.
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incorrectly converted to json
Fixed GO search to work with combined searches
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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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trait.py. Since I couldn't find the purpose of the assert statement I removed it.
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Fixes #69
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move duplicated code into a method,
handle the case of missing f1/f12 correctly
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Use NVD3 for bar chart and probability plot
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* z scores are computed on the client side (using jStat library)
* added Shapiro-Wilk test results
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some others)
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* 'aliases' and 'location' are shown only where relevant
* descriptions for phenotype datasets are provided at the top
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where rat trait pages wouldn't work
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it used to point to the now-renamed 'web' directory). It obviously also needs to be renamed later, but I'll have to find every place that calls webqtlConfig.HTMLPATH first to do so.
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other files
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