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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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Fixes #69
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move duplicated code into a method,
handle the case of missing f1/f12 correctly
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Added legend to bar chart color by trait function
Added scatterplot matrix figure
Fixed database timeout problem
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Fixed the header so that it looks fine when resizing
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Improved the appearance of the header menu and "title bar"
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On branch master
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or manhattan plot
Fixed a few minor bugs
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Conflicts:
wqflask/base/data_set.py
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Changed order of tabs in statistics panel on trait page
Started working on heatmap
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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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Suggestive/significant bars and additive effect curve added
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adding the correlation matrix page
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and storing the results in redis
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those with a lod score > 2
Did some work towards adding the colored backgrounds to chromosome
areas in the manhattan plot
Changed the last two chromosomes for human manhattan plots to
X and X/Y
Started work on writing a script that can independently run the
pyLMM code and store the results in redis
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Fixed some bug with generating the manhattan plot for the HLC data set
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Changed some code in dataset to try and track down the issue with Amelie's file
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on hover
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Correlation page now works with Non-BXD (or whatever group)
or All Samples options
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Conflicts:
wqflask/maintenance/quick_search_table.py
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There's just some issue with parents/f1s not being included if
you select non-BXD (or whatever the group is). All Samples, however
does work.
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For example, changed the two functions getting gene symbols and ids
for a dataset into one function that can take a column name as a
parameter
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correlation type (that is, when it is run again all traits in a
database)
Added a function to data_set.py that gets all the gene_ids in the
data set. Not sure if having a separate function for getting
the gene_ids and another for getting the gene symbols makes sense.
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the mapping, since it is reliable/fast and avoids us having to rewrite
from scratch using something like r/qtl
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in a dataset (in order to sort by tissue correlation instead of
sample correlation).
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manhattan plot
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they import (browser_test.py)
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Improved the templates for a couple pages related to changing user
password, etc
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