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path: root/wqflask/base/data_set.py
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2015-05-11Moving pylmm out of the treepjotrp
2015-03-17Converting an absolute path to a relative pathDannyArends
2015-01-30Fixed several bugsZachary Sloan
Added legend to bar chart color by trait function Added scatterplot matrix figure Fixed database timeout problem
2014-12-12Added a additive effect column to search result and collection tablesZachary Sloan
Fixed the header so that it looks fine when resizing
2014-11-17Just more changes converting to bootstrap 3Zachary Sloan
2014-10-17Added reference, policies, and links pagesZachary Sloan
Improved the appearance of the header menu and "title bar"
2014-08-21Committer: Lei Yan <lei@penguin.uthsc.edu>Lei Yan
On branch master
2014-08-21Added the option to display mapping results as either an interval mappingZachary Sloan
or manhattan plot Fixed a few minor bugs
2014-07-18Merge /home/zas1024/geneLei Yan
Conflicts: wqflask/base/data_set.py
2014-07-18Added outlier highlightingZachary Sloan
Changed order of tabs in statistics panel on trait page Started working on heatmap
2014-07-18Correlation table for phenotypes is workingLei Yan
2014-07-09Updated coffeescript, svg export working fine, interval mapping zoom workingZachary Sloan
2014-06-25Added Karl's correlation matrix codeZachary Sloan
Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
2014-06-06Implimented Karl Broman's lodchart code for the interval mapping function.Zachary Sloan
Suggestive/significant bars and additive effect curve added
2014-05-05Committing a bunch of changes related to integrating GEMMA andZachary Sloan
adding the correlation matrix page
2014-01-30Most of the work is done towards running lmm.py from the command lineZachary Sloan
and storing the results in redis
2014-01-29Limited number of markers in marker regression result table toZachary Sloan
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
2014-01-23Histogram is workingZachary Sloan
Fixed some bug with generating the manhattan plot for the HLC data set
2014-01-03Wrote some code for the histogram figureZachary Sloan
Changed some code in dataset to try and track down the issue with Amelie's file
2013-11-26Made some progress towards getting the traits inside a collection to display ↵Zachary Sloan
on hover
2013-11-25Got the interval mapping results into a tableZachary Sloan
2013-10-25Began working on color coding bar chart by extra attributesZachary Sloan
2013-10-15Changed templates to call the header macroZachary Sloan
Correlation page now works with Non-BXD (or whatever group) or All Samples options
2013-10-11Merge /home/lei/geneZachary Sloan
Conflicts: wqflask/maintenance/quick_search_table.py
2013-10-10Almost have correlation working for non-primary strain/groupLei Yan
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.
2013-10-09Improved some of the code related to the correlation pageLei Yan
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
2013-10-08Literature correlation works when it is selected as the sortedLei Yan
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.
2013-10-08Did some work with interval mapping page; will use qtl reaper to doZachary Sloan
the mapping, since it is reliable/fast and avoids us having to rewrite from scratch using something like r/qtl
2013-09-24Did some work towards doing the tissue correlation for all traitsroot
in a dataset (in order to sort by tissue correlation instead of sample correlation).
2013-08-21Just removed a couple print statementsZachary Sloan
2013-08-15Removed the markers with no variance (and thus no p-values) from theZachary Sloan
manhattan plot
2013-08-13Added several test files and the file with the class thatZachary Sloan
they import (browser_test.py)
2013-08-07Fixed things with the dataset dropdowns and mRNA datasetsZachary Sloan
Improved the templates for a couple pages related to changing user password, etc
2013-08-02Fixed a bug related to groups with genofiles (not sure if it makes senseZachary Sloan
for them not to have genofiles yet)
2013-07-30Just added some print statements to debug an issue with LMM codeZachary Sloan
Also added some to notes
2013-07-23Fixed a couple issues with he quick_search_table.py scriptZachary Sloan
Added notes on using percona to optimise mysql to gn_installation_notes.txt Started moving "get_trait_data" to DataSet since it is the same regardless of the particular DataSet subclass (PhenotypeDataSet, MrnaAssayDataSet, etc)
2013-07-19Finished integrating code that reads sample list from geno filesZachary Sloan
withouot using reaper and caches results so it doesn't need to read the file every single time someone loads a page
2013-07-19Created file gen_group_samplelists that iterates through all genofilesZachary Sloan
and builds each groups' samplelist
2013-07-16Wrote code that can get a dataset's type for every single GNZachary Sloan
dataset; previously we could not view traits in datasets that were not in the DBType table in the database
2013-06-27Created a group manager page where user administrators can createZachary Sloan
groups of datasets to give/add read privileges to
2013-06-26Moved code creating DataSets object to a function in dataset.pyZachary Sloan
Added caching to creating DataSets object
2013-06-26Got code that creates DataSets object runningZachary Sloan
Fixed one genofile that had extra quotation marks in the comments that caused an error Defaults mb_graph_interval to 1 for species without chromosome lengths in megabases
2013-06-25Added DataSets class to dataset.py that will be used to create list ofZachary Sloan
confidential datasets
2013-06-21Fixed bug where cursor was still being used in queryZachary Sloan
2013-06-19Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flaskZachary Sloan
Conflicts: wqflask/base/data_set.py wqflask/wqflask/views.py Fixed a couple conflicts to merge Lei's code related to the correlation page
2013-06-13Fixed issue where too much memory was used as a result of creating aLei Yan
dataset object for each trait in the correlation results Added new fields/columns for each trait in the correlation result table (max LRS, max LRS location, mean expression) Fixed error if trait doesn't have these fields
2013-06-12Fixed a couple issues with the template that caused theZachary Sloan
regular search results and show trait page to not display
2013-06-11Put trait info for correlation results page into a dictionary insteadLei Yan
of storing list of GeneralTrait objects Added print statements to track memory usage
2013-05-30Rewrote some code in get_trait_info in dataset.pyLei Yan
Added spearman correlation to show_corr_results and template
2013-05-28Have correlation values appearing in a table in the templateLei Yan
Use scipy to calculate pearson correlation instead of old GN code
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