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Metadata ignore subset columns #295

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7cc0731
"best" location for modalities bars legend
olgabot Jan 13, 2015
02ce439
set bar height to 0 if modality not detected
olgabot Jan 13, 2015
baa231c
fix number of modalities to always be the same
olgabot Jan 13, 2015
d8f9d19
fix width, linewidth and edgecolor
olgabot Jan 13, 2015
6fce6cc
Add percentages to study-level plot_modalities_bars
olgabot Jan 13, 2015
5bb02ae
add grid and ticklabels to modalities_bars figure
olgabot Jan 13, 2015
520b2ee
fix typo
olgabot Jan 13, 2015
dd21a84
add xlabel and ylabel
olgabot Jan 13, 2015
0590855
Add xlim
olgabot Jan 13, 2015
35f9d66
add plot_modalities_bars to gallery examples
olgabot Jan 13, 2015
e8424af
add groupbys to plot_modalities_reduced
olgabot Jan 13, 2015
ad16522
force modality assigments to always be a series
olgabot Jan 13, 2015
301ed26
removed groupby from plot_modalities_reduced invocation
olgabot Jan 13, 2015
424941e
add docstring
olgabot Jan 13, 2015
922a5e4
remove xticks and yticks from reduced space
olgabot Jan 13, 2015
20e5358
fix number of axes for modalities reduced plots
olgabot Jan 13, 2015
537ec9f
increase alpha
olgabot Jan 13, 2015
fc2280a
remove commented out pdb set trace
olgabot Jan 13, 2015
d0690de
add plot_modalities_reduced example
olgabot Jan 13, 2015
4b171eb
Add feature_ids to plot_modalities_lavalamps, and docstring
olgabot Jan 13, 2015
64d424a
add plot_event_modality_estimation to show logliks and bayes factors …
olgabot Jan 13, 2015
3325a94
fix call to modality_visualizer.event_estimation
olgabot Jan 14, 2015
bb5497a
add plot_modalities_lavalamps to gallery
olgabot Jan 14, 2015
10a709d
Fix build badge for Travis-CI
olgabot Jan 14, 2015
47ac671
add modality_colors to argument
olgabot Jan 14, 2015
16b35eb
fix reference to modality_colors
olgabot Jan 14, 2015
4d3a51f
fix logsumexps
olgabot Jan 14, 2015
77366f7
dropna for seaborn violinplot
olgabot Jan 14, 2015
ecb3ef2
move xlabel to loglik, fix formatting
olgabot Jan 14, 2015
930b2c4
Add renamed event id to event estimation plot
olgabot Jan 14, 2015
9bd11b4
add event ID using figtext which won't resize the axes
olgabot Jan 14, 2015
ff570c9
add xlabel to loglik for padding, change xticks of violin, smaller fo…
olgabot Jan 14, 2015
3801126
add phantom text for xlabel
olgabot Jan 14, 2015
20dbf41
turn on grid for ax_bayesfactor
olgabot Jan 14, 2015
ab0ba3d
Add plot example for plot_event_modality_estimation
olgabot Jan 14, 2015
833fb39
Add comment about readme badge in doc/releases/v0.2.5.txt
olgabot Jan 14, 2015
8524082
make font size smaller, add renamed to fig text
olgabot Jan 14, 2015
2ded4a8
change example for plot_event_modality_estimation
olgabot Jan 15, 2015
ba019c8
add uniform at _logsumexp step
olgabot Jan 15, 2015
b4d8535
Merge pull request #237 from YeoLab/readme_fixes
olgabot Jan 20, 2015
7207532
fix test_logsumexp test
olgabot Jan 20, 2015
5cd6aff
Add flag to py.test to show top 20 tests with the longest durations
olgabot Jan 20, 2015
61c8166
add numpydoc style docstrings to contributing.md
olgabot Jan 20, 2015
7c6f714
Merge branch 'bayesian_modalities'
olgabot Jan 20, 2015
ec0ad72
Merge branch 'master' of github.com:YeoLab/flotilla
olgabot Jan 20, 2015
bc19063
Initial commit for cosine transform pca
olgabot Jan 2, 2015
0e4368f
Move cosine transform code out of SplicingData.reduce() and into Spli…
olgabot Jan 20, 2015
f39983d
Removed SplicingData.reduce since now SplicingData._subset_and_standa…
olgabot Jan 20, 2015
e89cb91
Add test for SplicingData._subset_and_standardize
olgabot Jan 21, 2015
971b313
fix reduce bug
olgabot Jan 21, 2015
643f77c
Added Gitter badge
gitter-badger Jan 22, 2015
46fcdc8
Add example of pac splicing
olgabot Jan 23, 2015
e17613d
don't cache feature_renamer series
Jan 23, 2015
631a7c0
update plot_two_features and plot_two_samples tests to always use fe…
olgabot Jan 26, 2015
6c8d81c
properly access features with enough observations
olgabot Jan 26, 2015
a4b8bb6
properly except get_ipython()
olgabot Jan 26, 2015
265ee7e
Remove matplotlib inline call (user needs to do this themselves, and …
olgabot Jan 26, 2015
28ad908
update make lint call to not exclude everything
olgabot Jan 26, 2015
214c691
Add release note about removing ``matplotlib inline``
olgabot Jan 26, 2015
40cebad
Add cosine transform about splicing pca to release notes
olgabot Jan 26, 2015
c1646f6
Add docstring for SplicingData._subset_and_standardize
olgabot Jan 26, 2015
f7ef4c0
Fix up BaseData._subset_and_standardize docstring, with a concise one…
olgabot Jan 26, 2015
a5fc37c
remove whitespace for pep8
olgabot Jan 26, 2015
85c513f
Merge pull request #235 from YeoLab/splicing_pca
olgabot Jan 26, 2015
10f7f28
don't cache feature_renamer series
Jan 23, 2015
bc93f01
add a test for making sure feature_rename_col can change for feature_…
olgabot Jan 27, 2015
7e61b4b
Merge branch 'dont_cache_feature_renamer_series' of github.com:YeoLab…
olgabot Jan 27, 2015
04ddb11
Update makefile "lint" command to ignore __init__.py files
olgabot Jan 27, 2015
acdd8b8
Remove compute/visulaize/data_model imports from flotilla/__init__.py…
olgabot Jan 27, 2015
64772fe
Add __all__ statements to __init__.py so that make lint doesn't get mad
olgabot Jan 27, 2015
5d79984
Properly check if a file exists
olgabot Jan 27, 2015
9aa3eed
simple exception since "as e" isn't used
olgabot Jan 27, 2015
ad88300
remove variable assignment for validate_params
olgabot Jan 27, 2015
77237ea
comment out generate_scatter_table
olgabot Jan 27, 2015
d06630b
lint fixes
olgabot Jan 27, 2015
bf73a23
lint and more fixes for tests, but test (should) still pass
olgabot Jan 27, 2015
9d75d76
fix blank lines
olgabot Jan 27, 2015
7b9baa9
remove second command ot call pep8 on flotilla/test (redundant call)
olgabot Jan 27, 2015
d10e79f
pep8 fixes in flotilla/compute
olgabot Jan 27, 2015
082c90c
pep8 fixes, clean up all_true and all_false code
olgabot Jan 27, 2015
a559829
pep8 fixes, removed classify() memoize, hopefully addressing https://…
olgabot Jan 27, 2015
fcb0a3d
lint fixes in flotilla/data_model
olgabot Jan 27, 2015
2ccdeeb
pep8 fixes, remove generate_scatter_table
olgabot Jan 27, 2015
dd2136b
Fix to pep8 standards
olgabot Jan 27, 2015
95059a9
add lint, pep8 to testing script
olgabot Jan 27, 2015
fef17e5
move install commands around
olgabot Jan 27, 2015
42a2e4e
move install commands around
olgabot Jan 27, 2015
19ad6b5
Merge pull request #239 from gitter-badger/gitter-badge
olgabot Jan 27, 2015
98c9a86
move install commands around
olgabot Jan 27, 2015
7fbd5ea
Make comment about gitter badge
olgabot Jan 27, 2015
c748dad
move doc of classifier/regressor to use PredictorBase.__init__.__doc_…
olgabot Jan 27, 2015
8fa9933
Merge pull request #249 from YeoLab/dont_cache_feature_renamer_series
olgabot Jan 30, 2015
d95eb25
Merge branch 'lint_pep8'
olgabot Jan 30, 2015
d9e53c2
fix inconsequential merge conflict in base
olgabot Jan 30, 2015
42a297a
Add release note about scale_by_variance
olgabot Jan 26, 2015
2cf9780
Propagate scale_by_variance from DecompositionViz BaseData, Study.plo…
olgabot Jan 26, 2015
c1d7675
Change {reduced,violins}_fig to fig_{reduced,violins} for easy findin…
olgabot Jan 30, 2015
174a656
Initial commit for test_decomposition viz
olgabot Jan 30, 2015
7dc4227
{reduced,violins}_fig --> fig_{reduced,violins} for easy finding
olgabot Jan 30, 2015
dab3590
{reduced,violins}_fig --> fig_{reduced,violins}
olgabot Jan 30, 2015
a7689d2
dumb typo bug that was making the build fail
olgabot Jan 30, 2015
06f7a32
add indication that order and violinplot_kws are optional
olgabot Jan 30, 2015
81a4561
plot_violins=False, improve docstring of plot_dimensionality_reduction
olgabot Jan 30, 2015
39f4e5a
Change test_{decomposition,generic}.py --> test_{decomposition,generi…
olgabot Jan 30, 2015
8b6bb65
fix up Study.plot_pca docstring
olgabot Jan 30, 2015
9dd5186
pep8 fixes
olgabot Jan 30, 2015
02966de
Merge pull request #250 from YeoLab/scale_by_pca_variance
olgabot Jan 31, 2015
412cc6c
shorten test suite for testing of docs deployment
olgabot Feb 3, 2015
222e859
Update maturity used in the example classifier
olgabot Feb 3, 2015
e564505
Add simple push to travis yml
olgabot Feb 3, 2015
c9775e1
add brainspan data for plotting
olgabot Feb 3, 2015
a4721ee
fix getting of sample ids for trait
olgabot Feb 3, 2015
8e8c593
remove ax from plotting kwargs
olgabot Feb 3, 2015
abcee1b
change plot_classifier to use brainspan data
olgabot Feb 3, 2015
b90f8d5
add indexerror as possible error
olgabot Feb 3, 2015
312635d
restore test suite
olgabot Feb 4, 2015
69ca38c
change development docs branch back to master
olgabot Feb 4, 2015
65aad23
Merge pull request #254 from YeoLab/fix_docs
olgabot Feb 4, 2015
63ad940
only test one thing at a time...
olgabot Feb 4, 2015
9b06d85
Merge branch 'master' of github.com:YeoLab/flotilla
olgabot Feb 5, 2015
5cfc7f5
use npt to test instead of pdt
olgabot Feb 24, 2015
37d001e
Add warnings if the sample ids of subsets don't match up
olgabot Feb 24, 2015
e15c591
simplify tests
olgabot Feb 25, 2015
a9b0468
Add example gene ontology data
olgabot Feb 26, 2015
624f3b1
initial commit for gene ontology
olgabot Feb 3, 2015
a4d97c1
cleanup old ontology code
olgabot Feb 3, 2015
bd1dd7f
add docstring
olgabot Feb 26, 2015
f4037db
add logic to not try to createa GO database if gene_ontology_data is …
olgabot Feb 26, 2015
a073baa
Add status messages of building gene ontology database
olgabot Feb 26, 2015
3a4eec2
fix setting index
olgabot Feb 26, 2015
730f92e
add pdb set trace
olgabot Feb 26, 2015
384d063
few fixes
olgabot Feb 26, 2015
2087a81
change column names
olgabot Feb 26, 2015
f6d2ec3
reorganise GeneOntology data, create ontology in __init__, add option…
olgabot Feb 26, 2015
2117f28
add more options to go enrichment, fix up docstring
olgabot Feb 26, 2015
9ec93b5
stdout --> warnings
olgabot Feb 26, 2015
1073d16
Add go term domains and name to growing defaultdict, and return None …
olgabot Feb 26, 2015
cd2e250
make sure to create defaultdict properly
olgabot Feb 26, 2015
457c65e
df.empty is attribute, not method
olgabot Feb 26, 2015
861cfd8
also say error for why species data wasn't loaded
olgabot Feb 26, 2015
e72dba6
better error message
olgabot Feb 26, 2015
554c59d
access 0th value because 0th item by series may not be valid
olgabot Feb 26, 2015
ff28167
make sure provided domains are converted to frozenset, and fix logic …
olgabot Feb 26, 2015
b6300e4
also check that features of interest overlap with GO term
olgabot Feb 26, 2015
2143049
Make GeneOntologyData accessible from base flotilla
olgabot Feb 26, 2015
8c71cbf
Sort dataframe by p value
olgabot Feb 26, 2015
d8d4ea4
Add tests for gene ontology data
olgabot Feb 26, 2015
5cc8be4
fix tests after refactoring
olgabot Feb 27, 2015
2eabe5a
add example gene ontology data
olgabot Feb 27, 2015
d50b551
Fix tests and add more for a total of 98% coverage!
olgabot Feb 28, 2015
502375a
remove go.py (replaced with the data model)
olgabot Feb 28, 2015
66d8b81
Fix lint errors because pyflakes got majorly strict
olgabot Feb 28, 2015
7a68a43
remove plot_study_sample_legend because it's unused
olgabot Feb 28, 2015
0e6f05e
fix pep8
olgabot Feb 28, 2015
99187a1
fix bug addded while linting
olgabot Feb 28, 2015
b3d81df
speeding up test suite time
olgabot Feb 28, 2015
5393026
add more tests for Study
olgabot Feb 28, 2015
2b104cb
fix up plot_two_feature tests
olgabot Mar 4, 2015
fb27eb8
Add GO to release notes
olgabot Mar 4, 2015
ebc00d7
Merge pull request #266 from YeoLab/gene_ontology
olgabot Mar 4, 2015
bea9ca7
update date on release notes
olgabot Mar 4, 2015
726c128
Merge branch 'master' of github.com:YeoLab/flotilla
olgabot Mar 4, 2015
33a0f46
update version 0.2.5dev --> 0.2.5 for release
olgabot Mar 4, 2015
a3b9289
version bump to 0.2.6dev
olgabot Mar 4, 2015
4dd890f
save the GO data with the package
olgabot Mar 4, 2015
40bec13
start rewriting test for saving
olgabot Mar 4, 2015
0985a58
version down to 0.2.5 for fixing docs in release
olgabot Mar 4, 2015
2e20564
try to fix travis ci docs deployment
olgabot Mar 4, 2015
769aeed
version bump to 0.2.6dev
olgabot Mar 5, 2015
abc19be
shift bimodal and middle distributions to start with parameters more …
olgabot Mar 5, 2015
7e859b6
change min_samples to 10
olgabot Mar 5, 2015
c9d3e65
forgot parens around bimodal model parameters
olgabot Mar 5, 2015
a024c56
change min samples to default to 10 instead of 0.5
olgabot Mar 11, 2015
93a7fa3
Add ".data_original" to GeneOntologyData for compatibility with other…
olgabot Mar 12, 2015
23999a4
Fix up test for saving, add gene ontology data to study
olgabot Mar 12, 2015
259c656
Make Metadata's self.data_original point to self.data
olgabot Mar 12, 2015
1d3835b
save the minimum number of reads per sample, and save metadata's data…
olgabot Mar 12, 2015
6baf673
pep8 and lint fixes
olgabot Mar 12, 2015
714ab3c
add known genes from chr22 for testing
olgabot Mar 12, 2015
c04925f
Add release notes
olgabot Mar 12, 2015
5832ace
downgrade next version to 0.2.6 instead of 0.3.0 (not ready yet)
olgabot Mar 12, 2015
0b779f6
Merge pull request #271 from YeoLab/save_go_data
olgabot Mar 12, 2015
47f170a
Merged with master
olgabot Mar 12, 2015
cfd4abc
Fix creation of study in test
olgabot Mar 12, 2015
0bafb39
initial commit of supplemental data
olgabot Mar 12, 2015
7f4fac4
remove "_fixed", "_no_na" fixtures
olgabot Mar 12, 2015
4b86fc1
initial tests of supplemental seem to work
olgabot Mar 12, 2015
3e589dd
pep8 fixes (hopefully will fix failing tests)
olgabot Mar 12, 2015
5681048
lint fixes
olgabot Mar 12, 2015
ce93758
Add release notes
olgabot Mar 13, 2015
5dd63d3
Merge pull request #267 from YeoLab/shorten_test_suite_time
olgabot Mar 13, 2015
ce91f11
fix supplemental/spikein merge conflict
olgabot Mar 14, 2015
f3e1436
add release notes
olgabot Mar 16, 2015
3ca34ee
pep8 fixes
olgabot Mar 16, 2015
24c1fff
Add newline to sys.stdout message
olgabot Mar 16, 2015
d28eaaf
Add supplemental data to reading/loading of the datapackage
olgabot Mar 16, 2015
9040761
Add test for embarking on a datapackage with supplemental data
olgabot Mar 16, 2015
6e12d23
move _is_absolute_path to not a method of Study because it's needed d…
olgabot Mar 16, 2015
4e00dfc
initial addition of ipynb for supplementaldata
olgabot Mar 16, 2015
663ce48
Clarify where example plots should go, add requirement for new non-pl…
olgabot Mar 16, 2015
7bc0818
actually iterate over the items of name_to_df
olgabot Mar 16, 2015
054ba2e
fix resource --> supplemental in reading all supplemental data
olgabot Mar 16, 2015
986571a
Get supplemental resource name, not name of supplemental
olgabot Mar 16, 2015
b2aeaea
fix pep8
olgabot Mar 16, 2015
bb92407
Add option and test for user-specified flotilla directory
olgabot Mar 16, 2015
8c7705e
Add finished supplementaldata ipynb
olgabot Mar 16, 2015
8206a59
fix modality priors
olgabot Mar 16, 2015
f87e50b
Add docstrings and set minimum samples to be 10
olgabot Mar 16, 2015
75b54dc
Fix tests for modality assignments
olgabot Mar 16, 2015
164d2c5
fix pep8
olgabot Mar 16, 2015
e3ac7b5
merged up to master
olgabot Mar 16, 2015
4352e28
removed _fixed from test_splicingdata
olgabot Mar 16, 2015
8a5c59b
Merge pull request #276 from YeoLab/pr_checklist_examples
olgabot Mar 16, 2015
cdeb225
actually save the minimum number of samples
olgabot Mar 16, 2015
300a57e
Add release notes
olgabot Mar 16, 2015
b05ffc6
Add release notes about documenting
olgabot Mar 16, 2015
fc88ff0
Merge pull request #272 from YeoLab/supplemental_data
olgabot Mar 17, 2015
4afb11f
Add supplementaldata to tutorial
olgabot Mar 17, 2015
bfa166d
Merge pull request #278 from YeoLab/supplemental_data
olgabot Mar 17, 2015
a17486c
Move installing packages for documentation to only happen if this bra…
olgabot Mar 17, 2015
36453f1
Merge pull request #277 from YeoLab/study_save_min_samples
olgabot Mar 17, 2015
61ea979
Merge branch 'master' of github.com:YeoLab/flotilla
olgabot Mar 17, 2015
a788b66
fix pep8 errors created by removal of "_fixed"
olgabot Mar 17, 2015
6780653
add ipython notebook
olgabot Mar 18, 2015
63c398f
add modalities ipython notebook to tutorial.rst
olgabot Mar 18, 2015
d58b977
Add release notes
olgabot Mar 18, 2015
4552526
Merge branch 'master' into modality_priors
olgabot Mar 18, 2015
8fafe2a
Merge branch 'modality_priors'
olgabot Mar 18, 2015
ac92137
fix merge conflict in tutorial.rst and v0.2.6.rst
olgabot Mar 18, 2015
19208b3
remove mention of "scripts/" directory in PR checklist
olgabot Mar 18, 2015
4db36ee
add citation for PR checklist
olgabot Mar 18, 2015
17d153c
place the PCA legend in the "best" place
olgabot Mar 18, 2015
2f9e6e9
Add release notes about PCA legend
olgabot Mar 18, 2015
87293eb
Auto-expand plot_gene violins to the number of phenotypes
olgabot Apr 8, 2015
42cbcb8
Change default plotting markers from a circle to a variety of symbols
olgabot Apr 8, 2015
c653e55
Add "data_type" to error message of no feature id found
olgabot Apr 8, 2015
905cb68
Fix gridspec_kws --> gridspec_kw typo
olgabot Apr 8, 2015
c827e26
add tests for plot_gene, plot_event!
olgabot Apr 8, 2015
98eca91
fix test for metadata plotting markers
olgabot Apr 8, 2015
25d5cab
force phenotype_groupby to always be a series
olgabot Apr 8, 2015
5e8b7f1
Auto-adjust violin size in plot_pca
olgabot Apr 8, 2015
c71f086
Test plot_pca with violins
olgabot Apr 8, 2015
9030cca
Add release notes
olgabot Apr 8, 2015
b178977
Merge pull request #285 from YeoLab/variable_width_violin_plots
olgabot Apr 8, 2015
6d707d0
Add option to ignore columns in the metadata when making subsets of s…
olgabot Apr 10, 2015
ffaae65
started writing tests but they're broken
olgabot Apr 10, 2015
9ce0359
fix tests
olgabot Apr 10, 2015
7aa9053
change which data is accessed for tests of plot_two_samples
olgabot Apr 10, 2015
e7f0e6a
pep8 fixes
olgabot Jul 6, 2015
b6dcfb7
use six to check if ignore_subset_columns is a string or iterable
olgabot Jul 6, 2015
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plot_violins=False, improve docstring of plot_dimensionality_reduction
  • Loading branch information
olgabot committed Jan 30, 2015
commit 81a45617c2921d2e024f00d316b4f9989feea3de
61 changes: 40 additions & 21 deletions flotilla/data_model/base.py
Original file line number Diff line number Diff line change
@@ -494,7 +494,7 @@ def plot_classifier(self, trait, sample_ids=None, feature_ids=None,

def plot_dimensionality_reduction(self, x_pc=1, y_pc=2, sample_ids=None,
feature_ids=None, featurewise=False,
reducer=None, plot_violins=True,
reducer=None, plot_violins=False,
groupby=None, label_to_color=None,
label_to_marker=None, order=None,
reduce_kwargs=None, title='',
@@ -506,41 +506,59 @@ def plot_dimensionality_reduction(self, x_pc=1, y_pc=2, sample_ids=None,

Parameters
----------
x_pc : int, optional (default=1)
Which principal component to plot on the x-axis
y_pc : int, optional (default=2)
Which principal component to plot on the y-axis
sample_ids : list, optional (default=None)
x_pc : int, optional
Which principal component to plot on the x-axis (default 1)
y_pc : int, optional
Which principal component to plot on the y-axis (default 2)
sample_ids : list, optional
If None, plot all the samples. If a list of strings, must be
valid sample ids of the data.
feature_ids : list, optional (default=None)
valid sample ids of the data. (default None)
feature_ids : list, optional
If None, plot all the features. If a list of strings, perform and
plot dimensionality reduction on only these feature ids
featurewise : bool, optional (default=False)
Whether to keep the features and reduce on the samples (default
is to keep the samples and reduce the features)
featurewise : bool, optional
If True, the features are reduced on the samples, and the plotted
points are features, not samples. (default False)
reducer : :py:class:`.DataFrameReducerBase`, optional
(default=:py:class:`.DataFramePCA`)
Which decomposition object to use. Must be a child of
:py:class:`.DataFrameReducerBase` as this has built-in
compatibility with pandas.DataFrames.
plot_violins : bool, optional (default=True)
(default=:py:class:`.DataFramePCA`)
plot_violins : bool, optional
If True, plot the violinplots of the top features. This
can take a long time, so to save time you can turn it off if you
just want a quick look at the PCA.
groupby : mappable, optional (default=None)
just want a quick look at the PCA. (default False)
groupby : mappable, optional
Map each sample id to a group, such as a phenotype label
label_to_color : dict, optional (default=None)
(default None)
label_to_color : dict, optional
For each phenotype label, assign a color
label_to_marker : dict, optional (default=None)
(default None)
label_to_marker : dict, optional
For each phenotype label, assign a plotting marker symbol/shape
order : list, optional (default=None)
(default None)
order : list, optional
For violinplots, the order of the phenotype groups
color : list, optional (default=None)
For violinplots, the colors of the phenotypes in their order
(default None)
reduce_kwargs : dict, optional
Keyword arguments to the reducer (default None)
title : str, optional
Title of the reduced space plot (default '')
most_variant_features : bool, optional
If True, then only take the most variant of the provided features.
The most variant are determined by taking the features whose
variance is ``std_multiplier``standard deviations away from the
mean feature variance (default False)
std_multiplier : float, optional
If ``most_variant_features`` is True, then use this as a cutoff
for the minimum variance of a feature to be included (default 2)
scale_by_variance : bool, optional
If True, then scale the x- and y-axes by the explained variance
ratio of the principal component dimensions. Only valid for PCA
and its variations, not for NMF or tSNE. (default True)
plotting_kwargs : other keyword arguments
All other keyword arguments are passed to
:py:meth:`DecomopsitionViz.__call__`
:py:meth:`DecomopsitionViz.plot`

Returns
-------
@@ -553,6 +571,7 @@ def plot_dimensionality_reduction(self, x_pc=1, y_pc=2, sample_ids=None,
featurewise=featurewise,
reducer=reducer,
most_variant_features=most_variant_features,
std_multiplier=std_multiplier,
**reduce_kwargs)

visualized = DecompositionViz(reduced.reduced_space,