Flotilla
0.2.2
Tutorial
Gallery
YeoLab@UCSD
Site
flotilla
flotilla package
What’s new in the package
v0.2.1 (November 6th, 2014)
v0.2.0 (November 5th, 2014)
OS X Installation instructions
Docker Instructions
API Reference
General use plots
Interactive plots
Machine learning plots
Splicing-specific plots
Create your very own datapackage!
Flotilla tutorial
Install flotilla
Create a datapackage
Plotting functions
Recreated papers
Page
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
A
add_package_data_resource() (in module flotilla.util)
adjacency() (flotilla.compute.network.Networker method)
apply_calc_robust() (in module flotilla.compute.generic)
apply_calc_rs() (in module flotilla.compute.generic)
apply_calc_slope() (in module flotilla.compute.generic)
apply_dcor() (in module flotilla.compute.generic)
as_numpy() (in module flotilla.util)
AssertionError
assignments() (flotilla.compute.splicing.Modalities method)
B
bar() (flotilla.visualize.splicing.ModalitiesViz method)
BaseData (class in flotilla.data_model.base)
benjamini_hochberg() (in module flotilla.compute.expression)
big_nmf_space_transitions() (flotilla.data_model.base.BaseData method)
bin_range_strings() (in module flotilla.compute.infotheory)
binify() (flotilla.data_model.base.BaseData method)
(flotilla.data_model.expression.ExpressionData method)
(flotilla.data_model.splicing.SplicingData method)
(in module flotilla.compute.infotheory)
binned_nmf_reduced() (flotilla.data_model.base.BaseData method)
binned_reducer (flotilla.data_model.splicing.DownsampledSplicingData attribute)
(flotilla.data_model.splicing.SplicingData attribute)
builtin_predictor_configs (flotilla.compute.predict.PredictorConfigManager attribute)
C
cached_property (class in flotilla.util)
categorical (flotilla.compute.predict.Classifier attribute)
(flotilla.compute.predict.Regressor attribute)
celltype_event_counts (flotilla.data_model.study.Study attribute)
celltype_modalities (flotilla.data_model.study.Study attribute)
celltype_sizes() (flotilla.data_model.study.Study method)
check_a_feature() (flotilla.visualize.predict.ClassifierViz method)
check_if_already_downloaded() (in module flotilla.datapackage)
check_if_equal() (flotilla.compute.predict.PredictorDataSet method)
Classifier (class in flotilla.compute.predict)
ClassifierViz (class in flotilla.visualize.predict)
classify() (flotilla.data_model.base.BaseData method)
colors (flotilla.visualize.splicing.ModalitiesViz attribute)
compute_expression_splicing_covariance() (flotilla.data_model.study.Study method)
ConfigOptimizer (class in flotilla.compute.predict)
counts() (flotilla.compute.splicing.Modalities method)
D
data (flotilla.test.conftest.ExampleData attribute)
data_dir() (in module flotilla.test.conftest)
data_package_url_to_dict() (in module flotilla.datapackage)
DataFrameICA (class in flotilla.compute.decomposition)
DataFrameNMF (class in flotilla.compute.decomposition)
DataFramePCA (class in flotilla.compute.decomposition)
DataFrameReducerBase (class in flotilla.compute.decomposition)
DataFrameTSNE (class in flotilla.compute.decomposition)
dataset (flotilla.compute.predict.PredictorBase attribute)
dataset() (flotilla.compute.predict.PredictorDataSetManager method)
datasets (flotilla.compute.predict.PredictorDataSetManager attribute)
DecompositionViz (class in flotilla.visualize.decomposition)
default_feature_set_ids (flotilla.data_model.study.Study attribute)
default_feature_subsets (flotilla.data_model.study.Study attribute)
default_predictor_scoring_fun() (in module flotilla.compute.predict)
default_sample_subsets (flotilla.data_model.study.Study attribute)
default_score_cutoff_fun() (in module flotilla.compute.predict)
detect_outliers() (flotilla.data_model.base.BaseData method)
(flotilla.data_model.study.Study method)
dict_to_str() (in module flotilla.util)
do_pca() (flotilla.visualize.predict.PredictorBaseViz method)
do_r() (in module flotilla.compute.generic)
DownsampledSplicingData (class in flotilla.data_model.splicing)
draw_graph() (flotilla.visualize.network.NetworkerViz method)
draw_nonreduced_graph() (flotilla.visualize.network.NetworkerViz method)
drop_outliers() (flotilla.data_model.base.BaseData method)
(flotilla.data_model.study.Study method)
dropna_mean() (in module flotilla.compute.generic)
E
embark() (in module flotilla)
enrichment() (flotilla.go.GO method)
entropy() (in module flotilla.compute.infotheory)
event() (flotilla.visualize.splicing.ModalitiesViz method)
example_data() (in module flotilla.test.conftest)
example_datapackage() (in module flotilla.test.conftest)
example_datapackage_path() (in module flotilla.test.conftest)
example_study() (in module flotilla.test.conftest)
ExampleData (class in flotilla.test.conftest)
expression (flotilla.test.conftest.ExampleData attribute)
expression() (in module flotilla.test.conftest)
ExpressionData (class in flotilla.data_model.expression)
F
feature_renamer_series (flotilla.data_model.base.BaseData attribute)
feature_subset() (in module flotilla.test.conftest)
feature_subset_to_feature_ids() (flotilla.data_model.base.BaseData method)
(flotilla.data_model.study.Study method)
feature_subsets (flotilla.data_model.base.BaseData attribute)
fit() (flotilla.compute.decomposition.DataFrameNMF method)
(flotilla.compute.decomposition.DataFrameReducerBase method)
(flotilla.compute.predict.PredictorBase method)
fit_transform() (flotilla.compute.decomposition.DataFrameReducerBase method)
(flotilla.compute.decomposition.DataFrameTSNE method)
(flotilla.compute.splicing.Modalities method)
flotilla (module)
flotilla.compute (module)
flotilla.compute.decomposition (module)
flotilla.compute.expression (module)
flotilla.compute.generic (module)
flotilla.compute.infotheory (module)
flotilla.compute.network (module)
flotilla.compute.outlier (module)
flotilla.compute.predict (module)
flotilla.compute.splicing (module)
flotilla.data_model (module)
flotilla.data_model.base (module)
flotilla.data_model.expression (module)
flotilla.data_model.metadata (module)
flotilla.data_model.quality_control (module)
flotilla.data_model.splicing (module)
flotilla.data_model.study (module)
flotilla.datapackage (module)
flotilla.go (module)
flotilla.test (module)
flotilla.test.conftest (module)
flotilla.test.test_embark (module)
flotilla.test.test_util (module)
flotilla.util (module)
flotilla.visualize (module)
flotilla.visualize.color (module)
flotilla.visualize.decomposition (module)
flotilla.visualize.expression (module)
flotilla.visualize.generic (module)
flotilla.visualize.ipython_interact (module)
flotilla.visualize.network (module)
flotilla.visualize.predict (module)
flotilla.visualize.splicing (module)
from_datapackage() (flotilla.data_model.study.Study class method)
from_datapackage_file() (flotilla.data_model.study.Study class method)
from_datapackage_url() (flotilla.data_model.study.Study class method)
G
genelist_dropbox_link() (in module flotilla.test.conftest)
genelist_link() (in module flotilla.test.conftest)
genelist_path() (in module flotilla.test.conftest)
geneNames() (flotilla.go.GO method)
generate_scatter_table() (flotilla.visualize.predict.PredictorBaseViz method)
generateOntology() (in module flotilla.go)
get_boosting_regressor() (in module flotilla.compute.generic)
get_dcor() (in module flotilla.compute.generic)
get_feature_subsets() (flotilla.visualize.ipython_interact.Interactive static method)
get_loading_method() (in module flotilla.util)
get_regressor() (in module flotilla.compute.generic)
get_resource_from_name() (in module flotilla.datapackage)
get_robust_values() (in module flotilla.compute.generic)
get_slope() (in module flotilla.compute.generic)
get_switchy_score_order() (in module flotilla.compute.splicing)
get_unstarted_events() (in module flotilla.compute.generic)
get_weight_fun() (flotilla.compute.network.Networker method)
GO (class in flotilla.go)
GO_enrichment() (in module flotilla.go)
graph() (flotilla.compute.network.Networker method)
gstats() (flotilla.compute.expression.TwoWayGeneComparisonLocal method)
H
has_been_fit (flotilla.compute.predict.PredictorBase attribute)
has_been_scored (flotilla.compute.predict.PredictorBase attribute)
hist_single_vs_pooled_diff() (in module flotilla.visualize.splicing)
I
important_features_ (flotilla.compute.predict.PredictorBase attribute)
initializers (flotilla.data_model.study.Study attribute)
install_development_package() (in module flotilla.util)
Interactive (class in flotilla.visualize.ipython_interact)
interactive_choose_outliers() (flotilla.data_model.study.Study method)
(flotilla.Study method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_classifier() (flotilla.data_model.study.Study method)
(flotilla.Study method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_graph() (flotilla.data_model.study.Study method)
(flotilla.Study method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_lavalamp_pooled_inconsistent() (flotilla.data_model.study.Study method)
(flotilla.Study method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_localZ() (flotilla.visualize.ipython_interact.Interactive static method)
interactive_pca() (flotilla.data_model.study.Study method)
(flotilla.Study method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_plot_modalities_lavalamps() (flotilla.visualize.ipython_interact.Interactive static method)
interactive_reset_outliers() (flotilla.data_model.study.Study method)
(flotilla.Study method)
(flotilla.visualize.ipython_interact.Interactive static method)
J
jsd() (flotilla.data_model.study.Study method)
(in module flotilla.compute.infotheory)
K
kld() (in module flotilla.compute.infotheory)
L
lavalamp() (in module flotilla.visualize.splicing)
lavalamp_pooled_inconsistent() (in module flotilla.visualize.splicing)
link_to_geneNames() (flotilla.go.GO method)
link_to_list() (in module flotilla.util)
load() (in module flotilla.util)
load_csv() (in module flotilla.util)
load_gzip_pickle_df() (in module flotilla.util)
load_json() (in module flotilla.util)
load_pickle_df() (in module flotilla.util)
load_species_data() (flotilla.data_model.study.Study static method)
load_tsv() (in module flotilla.util)
M
make_feature_datapackage() (in module flotilla.datapackage)
make_study_datapackage() (in module flotilla.datapackage)
MappingStatsData (class in flotilla.data_model.quality_control)
max_feature_scaler() (flotilla.compute.predict.PredictorConfigScalers static method)
maybe_make_directory() (flotilla.data_model.study.Study static method)
maybe_renamed_to_feature_id() (flotilla.data_model.base.BaseData method)
memoize() (in module flotilla.util)
merge_boolean_columns() (flotilla.data_model.metadata.MetaData method)
MetaData (class in flotilla.data_model.metadata)
metadata (flotilla.test.conftest.ExampleData attribute)
Modalities (class in flotilla.compute.splicing)
modalities() (flotilla.data_model.splicing.SplicingData method)
(flotilla.data_model.study.Study method)
modalities_bins (flotilla.compute.splicing.Modalities attribute)
modalities_colors (flotilla.visualize.splicing.ModalitiesViz attribute)
modalities_counts() (flotilla.data_model.splicing.SplicingData method)
modalities_names (flotilla.compute.splicing.Modalities attribute)
modalities_order (flotilla.visualize.splicing.ModalitiesViz attribute)
ModalitiesViz (class in flotilla.visualize.splicing)
modality (flotilla.visualize.splicing.ModalitiesViz attribute)
N
n_components (flotilla.data_model.splicing.DownsampledSplicingData attribute)
(flotilla.data_model.splicing.SplicingData attribute)
n_estimators_scaler() (flotilla.compute.predict.PredictorConfigScalers static method)
n_good_features_ (flotilla.compute.predict.PredictorBase attribute)
n_jobs_scaler() (flotilla.compute.predict.PredictorConfigScalers static method)
n_phenotypes (flotilla.data_model.metadata.MetaData attribute)
natural_sort() (in module flotilla.util)
Networker (class in flotilla.compute.network)
NetworkerViz (class in flotilla.visualize.network)
new_dataset() (flotilla.compute.predict.PredictorDataSetManager method)
new_predictor_config() (flotilla.compute.predict.PredictorConfigManager method)
nmf() (flotilla.compute.predict.PredictorBase method)
nmf_space_positions() (flotilla.data_model.base.BaseData method)
nmf_space_transitions() (in module flotilla.visualize.generic)
normalize_to_spikein() (flotilla.data_model.study.Study method)
number_mapped (flotilla.data_model.quality_control.MappingStatsData attribute)
O
objective_average_times_seen() (flotilla.compute.predict.ConfigOptimizer static method)
oob_score_ (flotilla.compute.predict.PredictorBase attribute)
OutlierDetection (class in flotilla.compute.outlier)
outliers (flotilla.data_model.base.BaseData attribute)
P
parameters() (flotilla.compute.predict.PredictorConfig method)
pca() (flotilla.compute.predict.PredictorBase method)
percent_pooled_inconsistent() (flotilla.data_model.splicing.SplicingData method)
(flotilla.data_model.study.Study method)
percent_unique_celltype_events() (flotilla.data_model.study.Study method)
phenotype_color_order (flotilla.data_model.metadata.MetaData attribute)
phenotype_order (flotilla.data_model.metadata.MetaData attribute)
phenotype_transitions (flotilla.data_model.metadata.MetaData attribute)
plot() (flotilla.visualize.expression.TwoWayScatterViz method)
plot_big_nmf_space_transitions() (flotilla.data_model.base.BaseData method)
(flotilla.data_model.study.Study method)
plot_classifier() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
(flotilla.data_model.study.Study method)
plot_dimensionality_reduction() (flotilla.data_model.base.BaseData method)
plot_event() (flotilla.data_model.study.Study method)
(flotilla.Study method)
plot_explained_variance() (flotilla.visualize.decomposition.DecompositionViz method)
plot_feature() (flotilla.data_model.base.BaseData method)
(flotilla.data_model.splicing.SplicingData method)
plot_gene() (flotilla.data_model.study.Study method)
(flotilla.Study method)
plot_graph() (flotilla.data_model.study.Study method)
(flotilla.Study method)
plot_hist_single_vs_pooled_diff() (flotilla.data_model.splicing.SplicingData method)
plot_lavalamp_pooled_inconsistent() (flotilla.data_model.splicing.SplicingData method)
(flotilla.Study method)
(flotilla.data_model.study.Study method)
plot_loadings() (flotilla.visualize.decomposition.DecompositionViz method)
plot_modalities() (flotilla.data_model.study.Study method)
plot_modalities_bar() (flotilla.data_model.splicing.SplicingData method)
plot_modalities_lavalamps() (flotilla.data_model.splicing.SplicingData method)
(flotilla.data_model.study.Study method)
plot_modalities_reduced() (flotilla.data_model.splicing.SplicingData method)
plot_nmf_space_transitions() (flotilla.data_model.base.BaseData method)
plot_outliers() (flotilla.data_model.base.BaseData method)
plot_pca() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
(flotilla.data_model.study.Study method)
plot_pooled_dot() (in module flotilla.visualize.generic)
plot_reduced_space() (flotilla.visualize.splicing.ModalitiesViz method)
plot_regressor() (flotilla.data_model.study.Study method)
plot_samples() (flotilla.visualize.decomposition.DecompositionViz method)
plot_scores() (flotilla.visualize.predict.PredictorBaseViz method)
plot_study_sample_legend() (flotilla.data_model.study.Study method)
plot_two_features() (flotilla.data_model.base.BaseData method)
(flotilla.data_model.study.Study method)
plot_two_samples() (flotilla.data_model.base.BaseData method)
(flotilla.data_model.study.Study method)
plot_violins() (flotilla.visualize.decomposition.DecompositionViz method)
pooled (flotilla.data_model.base.BaseData attribute)
pooled_inconsistent() (flotilla.data_model.splicing.SplicingData method)
predict() (flotilla.compute.outlier.OutlierDetection method)
(flotilla.compute.predict.PredictorBase method)
predictor (flotilla.compute.predict.PredictorBase attribute)
predictor() (flotilla.compute.predict.PredictorDataSet method)
predictor_config() (flotilla.compute.predict.PredictorConfigManager method)
predictor_configs (flotilla.compute.predict.PredictorConfigManager attribute)
PredictorBase (class in flotilla.compute.predict)
PredictorBaseViz (class in flotilla.visualize.predict)
PredictorConfig (class in flotilla.compute.predict)
PredictorConfigManager (class in flotilla.compute.predict)
PredictorConfigScalers (class in flotilla.compute.predict)
PredictorDataSet (class in flotilla.compute.predict)
PredictorDataSetManager (class in flotilla.compute.predict)
predictors (flotilla.compute.predict.PredictorDataSet attribute)
R
raw_reducer (flotilla.data_model.splicing.DownsampledSplicingData attribute)
(flotilla.data_model.splicing.SplicingData attribute)
readers (flotilla.data_model.study.Study attribute)
reduce() (flotilla.data_model.base.BaseData method)
(flotilla.data_model.splicing.SplicingData method)
Regressor (class in flotilla.compute.predict)
RegressorViz (class in flotilla.visualize.predict)
relabel_pcs() (flotilla.compute.decomposition.DataFrameReducerBase static method)
S
sample_id_to_color (flotilla.data_model.metadata.MetaData attribute)
sample_id_to_phenotype (flotilla.data_model.metadata.MetaData attribute)
sample_subset_to_sample_ids() (flotilla.data_model.study.Study method)
sample_subsets (flotilla.data_model.metadata.MetaData attribute)
save() (flotilla.data_model.study.Study method)
score_coefficient (flotilla.compute.predict.PredictorBase attribute)
score_cutoff_ (flotilla.compute.predict.PredictorBase attribute)
scores_ (flotilla.compute.predict.PredictorBase attribute)
serve_ipython() (in module flotilla.util)
set_outliers_by_merging_columns() (flotilla.data_model.metadata.MetaData method)
set_reducer_plotting_args() (flotilla.visualize.predict.PredictorBaseViz method)
shared_events (flotilla.data_model.splicing.DownsampledSplicingData attribute)
shared_events_barplot() (flotilla.data_model.splicing.DownsampledSplicingData method)
shared_events_percentage() (flotilla.data_model.splicing.DownsampledSplicingData method)
shorten() (flotilla.visualize.decomposition.DecompositionViz method)
simple_twoway_scatter() (in module flotilla.visualize.generic)
singles (flotilla.data_model.base.BaseData attribute)
spearmanr_dataframe() (in module flotilla.compute.generic)
spearmanr_series() (in module flotilla.compute.generic)
SpikeInData (class in flotilla.data_model.expression)
SpliceJunctionData (class in flotilla.data_model.splicing)
splicing (flotilla.test.conftest.ExampleData attribute)
SplicingData (class in flotilla.data_model.splicing)
sqrt_jsd_modalities() (flotilla.compute.splicing.Modalities method)
Study (class in flotilla.data_model.study)
study() (in module flotilla.test.conftest)
subset_ (flotilla.compute.predict.PredictorBase attribute)
subsets_from_metadata() (in module flotilla.data_model.base)
switchy_score() (in module flotilla.compute.splicing)
T
test_embark() (in module flotilla.test.test_embark)
test_link_to_list() (in module flotilla.test.test_util)
timeout() (in module flotilla.util)
TimeoutError
timestamp() (in module flotilla.util)
to_base_file_tuple() (in module flotilla.util)
too_few_mapped (flotilla.data_model.quality_control.MappingStatsData attribute)
traitset (flotilla.compute.predict.PredictorDataSet attribute)
transform() (flotilla.compute.decomposition.DataFrameReducerBase method)
transition_distances() (flotilla.data_model.base.BaseData static method)
true_modalities (flotilla.compute.splicing.Modalities attribute)
TwoWayGeneComparisonLocal (class in flotilla.compute.expression)
TwoWayScatterViz (class in flotilla.visualize.expression)
U
unique_celltype_event_counts() (flotilla.data_model.study.Study method)
unique_phenotypes (flotilla.data_model.metadata.MetaData attribute)
V
validate_params() (in module flotilla.util)
variant (flotilla.data_model.base.BaseData attribute)
violinplot() (in module flotilla.visualize.generic)
W
weight_funs (flotilla.compute.network.Networker attribute)
write_csv() (in module flotilla.util)
write_gzip_pickle_df() (in module flotilla.util)
write_pickle_df() (in module flotilla.util)
write_tsv() (in module flotilla.util)
X
X (flotilla.compute.predict.PredictorBase attribute)
(flotilla.compute.predict.PredictorDataSet attribute)
Y
y (flotilla.compute.predict.PredictorBase attribute)
(flotilla.compute.predict.PredictorDataSet attribute)
Olga B. Botvinnik
is funded by the
NDSEG
fellowship and is a
NumFOCUS
John Hunter Technology Fellow
.
Michael T. Lovci was partially funded by a fellowship from
Genentech
. Partially funded by
NIH
grants NS075449 and HG004659 and
CIRM
grants RB4-06045 and TR3-05676 to
Gene Yeo
.