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Update violinplots to work with seaborn 0.6 #317

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Update violinplots to work with seaborn 0.6 #317

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@olgabot olgabot commented Jul 6, 2015

This allows for use of stripplot, which will plot individual observations in addition to the violins, like this;

image

  • 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:
    coverage run --source flotilla --omit=test --module py.test 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 the output of make lint.
  • Is it documented in the doc/releases/?
  • Was a spellchecker run on the source code and documentation after
    changes were made?

@olgabot
fix up plot_two_feature tests
2b104cb
@olgabot
Add GO to release notes
fb27eb8
@olgabot
Merge pull request #266 from YeoLab/gene_ontology
ebc00d7 
Gene ontology
@olgabot
update date on release notes
bea9ca7
@olgabot
Merge branch 'master' of github.com:YeoLab/flotilla
726c128 
* 'master' of github.com:YeoLab/flotilla: (31 commits)
  Add GO to release notes
  fix bug addded while linting
  fix pep8
  remove plot_study_sample_legend because it's unused
  Fix lint errors because pyflakes got majorly strict
  remove go.py (replaced with the data model)
  Fix tests and add more for  a total of 98% coverage!
  add example gene ontology data
  Add tests for gene ontology data
  Sort dataframe by p value
  Make GeneOntologyData accessible from base flotilla
  also check that features of interest overlap with GO term
  make sure provided domains are converted to frozenset, and fix logic for checking domain of GO term
  access 0th value because 0th item by series may not be valid
  better error message
  also say error for why species data wasn't loaded
  df.empty is attribute, not method
  make sure to create defaultdict properly
  Add go term domains and name to growing defaultdict, and return None if no GO categories were enriched
  stdout --> warnings
  ...
@olgabot
update version 0.2.5dev --> 0.2.5 for release
33a0f46
@olgabot
version bump to 0.2.6dev
a3b9289
@olgabot
save the GO data with the package
4dd890f
@olgabot
start rewriting test for saving
40bec13
@olgabot
version down to 0.2.5 for fixing docs in release
0985a58
@olgabot
try to fix travis ci docs deployment
2e20564
@olgabot
version bump to 0.2.6dev
769aeed
@olgabot
shift bimodal and middle distributions to start with parameters more …
abc19be 
…ddifferent than 1, and make bimodal an exponential prior
@olgabot
change min_samples to 10
7e859b6
@olgabot
forgot parens around bimodal model parameters
c9d3e65
@olgabot
change min samples to default to 10 instead of 0.5
a024c56
@olgabot
Add ".data_original" to GeneOntologyData for compatibility with other…
93a7fa3 
… datatypes
@olgabot
Fix up test for saving, add gene ontology data to study
23999a4
@olgabot
Make Metadata's self.data_original point to self.data
259c656
@olgabot
save the minimum number of reads per sample, and save metadata's data…
1d3835b 
…_original
@olgabot
pep8 and lint fixes
6baf673
@olgabot
add known genes from chr22 for testing
714ab3c
@olgabot
Add release notes
c04925f
@olgabot
downgrade next version to 0.2.6 instead of 0.3.0 (not ready yet)
5832ace
@olgabot
Merge pull request #271 from YeoLab/save_go_data
0b779f6 
Save GeneOntology data
@olgabot
Merged with master
47f170a
@olgabot
Fix creation of study in test
cfd4abc
@olgabot
initial commit of supplemental data
0bafb39
@olgabot
remove "_fixed", "_no_na" fixtures
7f4fac4
@olgabot
initial tests of supplemental seem to work
4b86fc1
olgabot added 28 commits May 28, 2015 09:47
@olgabot
Add release notes, fix naming and make sure releases are described in…
9f77583 
… Whats New
@olgabot
Merge pull request #308 from YeoLab/raster_lavalamp
b19728e 
By default, rasterize the lavalamp plot
@olgabot
Stepwise modality estimation
b3d02c4 
- Estimate Psi~{0,1} first, then bimodal and middle
- "uniform" --> "ambiguous"
- "excluded"/"included"--> "Psi~0"/"Psi~1"
@olgabot
Add tests for stepwise modality estimation
b2e69a8
@olgabot
Add stepwise modality estimation for a single event
71990dd
@olgabot
uniform --> ambiguous
aed3874
@olgabot
Close plots after plotting tests
7ef2cf8
@olgabot
whitespace for pep8
e4434fe
@olgabot
add release notes
dc990b9
@olgabot
Merge pull request #310 from YeoLab/stepwise_modalities
888c5f1 
Stepwise modalities
@olgabot
update all NMF and modality calculations to require 20 samples, fix b…
5448dea 
…ug for NMF space labeling
@olgabot
change number of samples to 50 for splicing testing
304959a
@olgabot
use n=20 as default instead of n=0.5
75f749e
@olgabot
fix tests for splicing modalities and NMF space
5c7cea3
@olgabot
update all NMF and modality calculations to require 20 samples, fix b…
7761406 
…ug for NMF space labeling
@olgabot
change number of samples to 50 for splicing testing
0a0e9ac
@olgabot
use n=20 as default instead of n=0.5
6946175
@olgabot
fix tests for splicing modalities and NMF space
65703c4
@olgabot
if there are zero non-NA values in a dataset, make sure all its log b…
5bed758 
…fs are NA
@olgabot
Merge remote-tracking branch 'origin/splicing_min20' into splicing_min20
0f57cf9 
* origin/splicing_min20:
  fix tests for splicing modalities and NMF space
  use n=20 as default instead of n=0.5
  change number of samples to 50 for splicing testing
  update all NMF and modality calculations to require 20 samples, fix bug for NMF space labeling
@olgabot
don't estimate modalities on data iwth no counts
e742b7c
@olgabot
Add violinplots from temposeq ipython
ccedfb6
@olgabot
Require seaborn 0.6 for violinplot and stripplot
c2100a6
@olgabot
fix logic
4c752f6
@olgabot
Add docstrings
3fd682c
@olgabot
Add splicing-specific parameters for violinplots in plot_feature
c3b6c68
@olgabot
propagate changes to BaseData._violinplot
a0f57a4
@olgabot
lint fixes
a65151c
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