Metadata marker #297

olgabot · 2015-04-10T16:47:23Z

fix saving markers from metadata

Is it mergable?
Did it pass the tests?
If it introduces new functionality in is it tested?
Check for code coverage. To run code coverage on only the file you changed,
for example flotilla/compute/splicing.py, use this command:
py.test --cov flotilla/compute/splicing.py --cov-report term-missing flotilla/test/compute/test_splicing.py
which will show you which lines aren't covered by the tests.
Do the new functions have descriptive
numpydoc
style docstrings?
If it adds a new feature, is it documented as an IPython Notebook in
examples/, and is that notebook added to doc/tutorial.rst?
If it adds a new plot, is it documented in the gallery, as a .py file
in examples/?
Is it well formatted? Look at make pep8 and make lint output
Is it documented in the doc/releases/?
Was a spellchecker run on the source code and documentation after
changes were made?

README fixes

* bayesian_modalities: (78 commits) Add flag to py.test to show top 20 tests with the longest durations fix test_logsumexp test add uniform at _logsumexp step change example for plot_event_modality_estimation make font size smaller, add renamed to fig text Add plot example for plot_event_modality_estimation turn on grid for ax_bayesfactor add phantom text for xlabel add xlabel to loglik for padding, change xticks of violin, smaller font for figtext add event ID using figtext which won't resize the axes Add renamed event id to event estimation plot move xlabel to loglik, fix formatting dropna for seaborn violinplot fix logsumexps fix reference to modality_colors add modality_colors to argument add plot_modalities_lavalamps to gallery fix call to modality_visualizer.event_estimation add plot_event_modality_estimation to show logliks and bayes factors for a modality Add feature_ids to plot_modalities_lavalamps, and docstring ...

* 'master' of github.com:YeoLab/flotilla: Add comment about readme badge in doc/releases/v0.2.5.txt Fix build badge for Travis-CI added feature standardization to cluster plot by default added feature standardization to cluster plot by default remove references to local server changed to s3 destination for metadata fixed feature_renamer for strings

…cingData._subset_and_standardize so it's accessible to all functions which require standardized data

…rdize does a cosine transform

…tures/samples with at least 10 observations

…it messes up "make lint")

…-line summary, then a longer summary beneath. And change language of boolean from "whether or not" to "If True, .."

Flexible plotting with many samples

* decomposition_heatmap_pcs: (31 commits) Add release notes pep8 fixes Add a feature renamer if there wasn't one Actually test if things were plotted to the axes add release notes pep8+docstrings Add docstring for plot Fix pep8, add docstring Add release notes Despine only the scatter and line plots, not the the heatmap add colorbar label shrink yticklabels down to 11 pt font shrink yticklabels of PC heatmap down to 12 (from 13) revert back to when figure was "good enough" Add another column to gridspec, remove ax_empty increase wspace, hspace, actually get yticklabels make yticklabels of heatmap smaller change wspace and hspace to 0 make explained variance ratio graph shorter fix ax pcs colorbar ...

…ored

…phenotype_order

coveralls · 2015-04-10T17:18:58Z

Coverage decreased (-0.0%) to 53.73% when pulling 947ed16 on metadata_marker into dfec06b on master.

coveralls · 2015-04-10T17:54:05Z

Coverage decreased (-0.0%) to 53.73% when pulling 947ed16 on metadata_marker into dfec06b on master.

olgabot and others added 30 commits January 13, 2015 17:37

turn on grid for ax_bayesfactor

20dbf41

Add plot example for plot_event_modality_estimation

ab0ba3d

Add comment about readme badge in doc/releases/v0.2.5.txt

833fb39

make font size smaller, add renamed to fig text

8524082

change example for plot_event_modality_estimation

2ded4a8

add uniform at _logsumexp step

ba019c8

Merge pull request #237 from YeoLab/readme_fixes

b4d8535

README fixes

fix test_logsumexp test

7207532

Add flag to py.test to show top 20 tests with the longest durations

5cd6aff

add numpydoc style docstrings to contributing.md

61c8166

Initial commit for cosine transform pca

bc19063

Move cosine transform code out of SplicingData.reduce() and into Spli…

0e4368f

…cingData._subset_and_standardize so it's accessible to all functions which require standardized data

Removed SplicingData.reduce since now SplicingData._subset_and_standa…

f39983d

…rdize does a cosine transform

Add test for SplicingData._subset_and_standardize

e89cb91

fix reduce bug

971b313

Added Gitter badge

643f77c

Add example of pac splicing

46fcdc8

don't cache feature_renamer series

e17613d

update plot_two_features and plot_two_samples tests to always use fea…

631a7c0

…tures/samples with at least 10 observations

properly access features with enough observations

6c8d81c

properly except get_ipython()

a4b8bb6

Remove matplotlib inline call (user needs to do this themselves, and …

265ee7e

…it messes up "make lint")

update make lint call to not exclude everything

28ad908

Add release note about removing matplotlib inline

214c691

Add cosine transform about splicing pca to release notes

40cebad

Add docstring for SplicingData._subset_and_standardize

c1646f6

Fix up BaseData._subset_and_standardize docstring, with a concise one…

f7ef4c0

…-line summary, then a longer summary beneath. And change language of boolean from "whether or not" to "If True, .."

remove whitespace for pep8

a5fc37c

olgabot added 24 commits March 18, 2015 11:58

remove mention of "scripts/" directory in PR checklist

19208b3

add citation for PR checklist

4db36ee

place the PCA legend in the "best" place

17d153c

Add release notes about PCA legend

2f9e6e9

Auto-expand plot_gene violins to the number of phenotypes

87293eb

Change default plotting markers from a circle to a variety of symbols

42cbcb8

Add "data_type" to error message of no feature id found

c653e55

Fix gridspec_kws --> gridspec_kw typo

905cb68

add tests for plot_gene, plot_event!

c827e26

fix test for metadata plotting markers

98eca91

force phenotype_groupby to always be a series

25d5cab

Auto-adjust violin size in plot_pca

5e8b7f1

Test plot_pca with violins

c71f086

Add release notes

9030cca

Merge pull request #285 from YeoLab/variable_width_violin_plots

b178977

Flexible plotting with many samples

Actually test if things were plotted to the axes

510051b

Add a feature renamer if there wasn't one

6afcc34

pep8 fixes

2b406df

Add release notes

9e46069

fix merge conflict (more things in release ntoes

9efbcbd

add new markers to MetaData._phenotype_to_marker which is actually st…

9333972

…ored

add all other phenotypes to in unique phenotypes besides the ones in …

7e1d5a6

…phenotype_order

remove marker making code from MetaData.__init__

533f9f6

olgabot added the in progress label Apr 10, 2015

pep8 fixes

947ed16

pep8 fixes

7fc9496

olgabot force-pushed the master branch from 8f79ec6 to 0a903c2 Compare July 7, 2015 15:45

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Metadata marker #297

Metadata marker #297

olgabot commented Apr 10, 2015

coveralls commented Apr 10, 2015

coveralls commented Apr 10, 2015

Metadata marker #297

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Metadata marker #297

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olgabot commented Apr 10, 2015

coveralls commented Apr 10, 2015

coveralls commented Apr 10, 2015