From 72d85f3c5ac60db12b601b10f9f6cb3ff725b8e3 Mon Sep 17 00:00:00 2001 From: gunthergl Date: Tue, 16 Apr 2024 01:06:39 +0000 Subject: [PATCH] deploy: 8b8ad76b2daaecd336a53410e2f0b306606cc449 --- .buildinfo | 2 +- _modules/index.html | 4 +-- _modules/nbnode/apply/count_celltree_df.html | 4 +-- _modules/nbnode/apply/gate_csv.html | 4 +-- _modules/nbnode/io/pickle_open_dump.html | 4 +-- _modules/nbnode/nbnode.html | 4 +-- _modules/nbnode/nbnode_trees.html | 4 +-- _modules/nbnode/nbnode_util.html | 4 +-- _modules/nbnode/plot/shifted_colormap.html | 4 +-- _modules/nbnode/plot/utils.html | 4 +-- .../nbnode/simulation/FlowSimulationTree.html | 4 +-- .../TreeMeanDistributionSampler.html | 4 +-- .../nbnode/simulation/TreeMeanRelative.html | 4 +-- .../nbnode/simulation/sim_proportional.html | 4 +-- _modules/nbnode/simulation/sim_target.html | 4 +-- .../intraassay/gate_init.html | 4 +-- .../intraassay/sims/sim00.html | 4 +-- .../intraassay/sims/sim01.html | 4 +-- .../intraassay/sims/sim02.html | 4 +-- .../intraassay/sims/sim03.html | 4 +-- _modules/nbnode/testutil/helpers.html | 4 +-- _modules/nbnode/utils/merge_leaf_nodes.html | 4 +-- _static/documentation_options.js | 2 +- api/modules.html | 4 +-- api/nbnode.apply.html | 6 ++-- api/nbnode.html | 14 ++++---- api/nbnode.io.html | 4 +-- api/nbnode.plot.html | 6 ++-- api/nbnode.simulation.html | 30 +++++++++--------- api/nbnode.specific_analyses.html | 4 +-- api/nbnode.specific_analyses.intraassay.html | 6 ++-- ...ode.specific_analyses.intraassay.sims.html | 4 +-- api/nbnode.testutil.html | 4 +-- api/nbnode.utils.html | 6 ++-- authors.html | 4 +-- changelog.html | 4 +-- contributing.html | 4 +-- genindex.html | 4 +-- index.html | 4 +-- license.html | 4 +-- notebooks.html | 4 +-- notebooks/nbnode-01.html | 4 +-- notebooks/nbnode-02.html | 4 +-- notebooks/nbnode-03.html | 4 +-- notebooks/nbnode-04.html | 4 +-- notebooks/nbnode-05_sim.html | 4 +-- objects.inv | Bin 4442 -> 4437 bytes py-modindex.html | 4 +-- readme.html | 4 +-- search.html | 4 +-- 50 files changed, 118 insertions(+), 118 deletions(-) diff --git a/.buildinfo b/.buildinfo index fd0f1b6..bf902ce 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 92d3a67d10f096f535fafca55bd153c1 +config: 7c30bcaf7cb1f5984d648d12b3e27dcf tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_modules/index.html b/_modules/index.html index a2dc90b..62486bf 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -4,10 +4,10 @@ - Overview: module code — nbnode 0.0.post1.dev1 documentation + Overview: module code — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/apply/count_celltree_df.html b/_modules/nbnode/apply/count_celltree_df.html index 28e0b99..860eb1f 100644 --- a/_modules/nbnode/apply/count_celltree_df.html +++ b/_modules/nbnode/apply/count_celltree_df.html @@ -4,10 +4,10 @@ - nbnode.apply.count_celltree_df — nbnode 0.0.post1.dev1 documentation + nbnode.apply.count_celltree_df — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/apply/gate_csv.html b/_modules/nbnode/apply/gate_csv.html index 0667c79..650f990 100644 --- a/_modules/nbnode/apply/gate_csv.html +++ b/_modules/nbnode/apply/gate_csv.html @@ -4,10 +4,10 @@ - nbnode.apply.gate_csv — nbnode 0.0.post1.dev1 documentation + nbnode.apply.gate_csv — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/io/pickle_open_dump.html b/_modules/nbnode/io/pickle_open_dump.html index 8690f3b..0f55b8a 100644 --- a/_modules/nbnode/io/pickle_open_dump.html +++ b/_modules/nbnode/io/pickle_open_dump.html @@ -4,10 +4,10 @@ - nbnode.io.pickle_open_dump — nbnode 0.0.post1.dev1 documentation + nbnode.io.pickle_open_dump — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/nbnode.html b/_modules/nbnode/nbnode.html index d22714d..568a802 100644 --- a/_modules/nbnode/nbnode.html +++ b/_modules/nbnode/nbnode.html @@ -4,10 +4,10 @@ - nbnode.nbnode — nbnode 0.0.post1.dev1 documentation + nbnode.nbnode — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/nbnode_trees.html b/_modules/nbnode/nbnode_trees.html index c4e95fe..d626ea7 100644 --- a/_modules/nbnode/nbnode_trees.html +++ b/_modules/nbnode/nbnode_trees.html @@ -4,10 +4,10 @@ - nbnode.nbnode_trees — nbnode 0.0.post1.dev1 documentation + nbnode.nbnode_trees — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/nbnode_util.html b/_modules/nbnode/nbnode_util.html index fe694af..cbddd57 100644 --- a/_modules/nbnode/nbnode_util.html +++ b/_modules/nbnode/nbnode_util.html @@ -4,10 +4,10 @@ - nbnode.nbnode_util — nbnode 0.0.post1.dev1 documentation + nbnode.nbnode_util — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/plot/shifted_colormap.html b/_modules/nbnode/plot/shifted_colormap.html index 4289846..eb5affe 100644 --- a/_modules/nbnode/plot/shifted_colormap.html +++ b/_modules/nbnode/plot/shifted_colormap.html @@ -4,10 +4,10 @@ - nbnode.plot.shifted_colormap — nbnode 0.0.post1.dev1 documentation + nbnode.plot.shifted_colormap — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/plot/utils.html b/_modules/nbnode/plot/utils.html index a35c2da..ff67dba 100644 --- a/_modules/nbnode/plot/utils.html +++ b/_modules/nbnode/plot/utils.html @@ -4,10 +4,10 @@ - nbnode.plot.utils — nbnode 0.0.post1.dev1 documentation + nbnode.plot.utils — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/simulation/FlowSimulationTree.html b/_modules/nbnode/simulation/FlowSimulationTree.html index 7448bf3..5cd2879 100644 --- a/_modules/nbnode/simulation/FlowSimulationTree.html +++ b/_modules/nbnode/simulation/FlowSimulationTree.html @@ -4,10 +4,10 @@ - nbnode.simulation.FlowSimulationTree — nbnode 0.0.post1.dev1 documentation + nbnode.simulation.FlowSimulationTree — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/simulation/TreeMeanDistributionSampler.html b/_modules/nbnode/simulation/TreeMeanDistributionSampler.html index 018ac8a..bc4caa1 100644 --- a/_modules/nbnode/simulation/TreeMeanDistributionSampler.html +++ b/_modules/nbnode/simulation/TreeMeanDistributionSampler.html @@ -4,10 +4,10 @@ - nbnode.simulation.TreeMeanDistributionSampler — nbnode 0.0.post1.dev1 documentation + nbnode.simulation.TreeMeanDistributionSampler — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/simulation/TreeMeanRelative.html b/_modules/nbnode/simulation/TreeMeanRelative.html index 3dd8ba5..2213537 100644 --- a/_modules/nbnode/simulation/TreeMeanRelative.html +++ b/_modules/nbnode/simulation/TreeMeanRelative.html @@ -4,10 +4,10 @@ - nbnode.simulation.TreeMeanRelative — nbnode 0.0.post1.dev1 documentation + nbnode.simulation.TreeMeanRelative — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/simulation/sim_proportional.html b/_modules/nbnode/simulation/sim_proportional.html index 2703dfa..a940578 100644 --- a/_modules/nbnode/simulation/sim_proportional.html +++ b/_modules/nbnode/simulation/sim_proportional.html @@ -4,10 +4,10 @@ - nbnode.simulation.sim_proportional — nbnode 0.0.post1.dev1 documentation + nbnode.simulation.sim_proportional — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/simulation/sim_target.html b/_modules/nbnode/simulation/sim_target.html index fad9854..24bbc51 100644 --- a/_modules/nbnode/simulation/sim_target.html +++ b/_modules/nbnode/simulation/sim_target.html @@ -4,10 +4,10 @@ - nbnode.simulation.sim_target — nbnode 0.0.post1.dev1 documentation + nbnode.simulation.sim_target — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/specific_analyses/intraassay/gate_init.html b/_modules/nbnode/specific_analyses/intraassay/gate_init.html index 7eb18fb..5ff1396 100644 --- a/_modules/nbnode/specific_analyses/intraassay/gate_init.html +++ b/_modules/nbnode/specific_analyses/intraassay/gate_init.html @@ -4,10 +4,10 @@ - nbnode.specific_analyses.intraassay.gate_init — nbnode 0.0.post1.dev1 documentation + nbnode.specific_analyses.intraassay.gate_init — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/specific_analyses/intraassay/sims/sim00.html b/_modules/nbnode/specific_analyses/intraassay/sims/sim00.html index 20f10b2..395fd0e 100644 --- a/_modules/nbnode/specific_analyses/intraassay/sims/sim00.html +++ b/_modules/nbnode/specific_analyses/intraassay/sims/sim00.html @@ -4,10 +4,10 @@ - nbnode.specific_analyses.intraassay.sims.sim00 — nbnode 0.0.post1.dev1 documentation + nbnode.specific_analyses.intraassay.sims.sim00 — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/specific_analyses/intraassay/sims/sim01.html b/_modules/nbnode/specific_analyses/intraassay/sims/sim01.html index 50b9a7e..747cda4 100644 --- a/_modules/nbnode/specific_analyses/intraassay/sims/sim01.html +++ b/_modules/nbnode/specific_analyses/intraassay/sims/sim01.html @@ -4,10 +4,10 @@ - nbnode.specific_analyses.intraassay.sims.sim01 — nbnode 0.0.post1.dev1 documentation + nbnode.specific_analyses.intraassay.sims.sim01 — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/specific_analyses/intraassay/sims/sim02.html b/_modules/nbnode/specific_analyses/intraassay/sims/sim02.html index 9946334..7886c2f 100644 --- a/_modules/nbnode/specific_analyses/intraassay/sims/sim02.html +++ b/_modules/nbnode/specific_analyses/intraassay/sims/sim02.html @@ -4,10 +4,10 @@ - nbnode.specific_analyses.intraassay.sims.sim02 — nbnode 0.0.post1.dev1 documentation + nbnode.specific_analyses.intraassay.sims.sim02 — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/specific_analyses/intraassay/sims/sim03.html b/_modules/nbnode/specific_analyses/intraassay/sims/sim03.html index 46a74c4..a4e31fc 100644 --- a/_modules/nbnode/specific_analyses/intraassay/sims/sim03.html +++ b/_modules/nbnode/specific_analyses/intraassay/sims/sim03.html @@ -4,10 +4,10 @@ - nbnode.specific_analyses.intraassay.sims.sim03 — nbnode 0.0.post1.dev1 documentation + nbnode.specific_analyses.intraassay.sims.sim03 — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/testutil/helpers.html b/_modules/nbnode/testutil/helpers.html index 9b69702..f01ab80 100644 --- a/_modules/nbnode/testutil/helpers.html +++ b/_modules/nbnode/testutil/helpers.html @@ -4,10 +4,10 @@ - nbnode.testutil.helpers — nbnode 0.0.post1.dev1 documentation + nbnode.testutil.helpers — nbnode 0.0.post1 documentation - + diff --git a/_modules/nbnode/utils/merge_leaf_nodes.html b/_modules/nbnode/utils/merge_leaf_nodes.html index 455053f..6b77f4a 100644 --- a/_modules/nbnode/utils/merge_leaf_nodes.html +++ b/_modules/nbnode/utils/merge_leaf_nodes.html @@ -4,10 +4,10 @@ - nbnode.utils.merge_leaf_nodes — nbnode 0.0.post1.dev1 documentation + nbnode.utils.merge_leaf_nodes — nbnode 0.0.post1 documentation - + diff --git a/_static/documentation_options.js b/_static/documentation_options.js index c7a8b73..06c3ace 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '0.0.post1.dev1', + VERSION: '0.0.post1', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/api/modules.html b/api/modules.html index 3373d28..a8ea7f9 100644 --- a/api/modules.html +++ b/api/modules.html @@ -5,10 +5,10 @@ - nbnode — nbnode 0.0.post1.dev1 documentation + nbnode — nbnode 0.0.post1 documentation - + diff --git a/api/nbnode.apply.html b/api/nbnode.apply.html index 27eacef..3135e76 100644 --- a/api/nbnode.apply.html +++ b/api/nbnode.apply.html @@ -5,10 +5,10 @@ - nbnode.apply package — nbnode 0.0.post1.dev1 documentation + nbnode.apply package — nbnode 0.0.post1 documentation - + @@ -41,7 +41,7 @@

Submodules

nbnode.apply.count_celltree_df module

-nbnode.apply.count_celltree_df.count_celltree_df(celltree_gated: NBNode) → DataFrame[source]
+nbnode.apply.count_celltree_df.count_celltree_df(celltree_gated: NBNode) → DataFrame[source]

Count the number of rows in node.data (per node) grouped by “sample_name” and concat them into a dataframe

diff --git a/api/nbnode.html b/api/nbnode.html index 3f264a9..8aa324b 100644 --- a/api/nbnode.html +++ b/api/nbnode.html @@ -5,10 +5,10 @@ - nbnode package — nbnode 0.0.post1.dev1 documentation + nbnode package — nbnode 0.0.post1 documentation - + @@ -283,7 +283,7 @@

Submodules
-property data: DataFrame
+property data: DataFrame

Data of a node for its ids.

root._data contains all data. However, each node only “holds” a subset of the data. To not have to copy the data for each node, we just subset the data @@ -351,7 +351,7 @@

Submodules
-export_counts(only_leafnodes: bool = False, node_counts_dtype='int64') → DataFrame[source]
+export_counts(only_leafnodes: bool = False, node_counts_dtype='int64') → DataFrame[source]

Export the counts of the predicted celltree to a pd.Dataframe.

Rows are the samples, columns the node names get_name_full()

@@ -500,7 +500,7 @@

Submodules
-predict(values: List | Dict | DataFrame | None = None, names: list | None = None, allow_unfitting_data: bool = False, allow_part_predictions: bool = False) → NBNode | List[NBNode] | Series[source]
+predict(values: List | Dict | DataFrame | None = None, names: list | None = None, allow_unfitting_data: bool = False, allow_part_predictions: bool = False) → NBNode | List[NBNode] | Series[source]

See single_prediction.

But you can put in dataframes or ndarrays instead of only dict + value/key paired lists.

@@ -1013,7 +1013,7 @@

Submodules

nbnode.nbnode_util module

-nbnode.nbnode_util.frame_cov(dt_frame: Frame) → DataFrame[source]
+nbnode.nbnode_util.frame_cov(dt_frame: Frame) → DataFrame[source]

Compute the covariance matrix of a datatable frame from all columns.

Similar to pd.DataFrame.cov().

@@ -1031,7 +1031,7 @@

Submodules
-nbnode.nbnode_util.per_node_data_fun(x: DataFrame, fun_name: str, include_features: List[str | int] | slice | None = None, *fun_args, **fun_kwargs) → DataFrame | Any[source]
+nbnode.nbnode_util.per_node_data_fun(x: DataFrame, fun_name: str, include_features: List[str | int] | slice | None = None, *fun_args, **fun_kwargs) → DataFrame | Any[source]

per_node_data_fun.

To be used in NBnode.node.apply() to apply a function to the data of each node.

diff --git a/api/nbnode.io.html b/api/nbnode.io.html index ca51e31..9fbba40 100644 --- a/api/nbnode.io.html +++ b/api/nbnode.io.html @@ -5,10 +5,10 @@ - nbnode.io package — nbnode 0.0.post1.dev1 documentation + nbnode.io package — nbnode 0.0.post1 documentation - + diff --git a/api/nbnode.plot.html b/api/nbnode.plot.html index 60f09bf..c134550 100644 --- a/api/nbnode.plot.html +++ b/api/nbnode.plot.html @@ -5,10 +5,10 @@ - nbnode.plot package — nbnode 0.0.post1.dev1 documentation + nbnode.plot package — nbnode 0.0.post1 documentation - + @@ -41,7 +41,7 @@

Submodules

nbnode.plot.shifted_colormap module

-nbnode.plot.shifted_colormap.shifted_colormap(cmap, min_val, max_val, name) → Colormap[source]
+nbnode.plot.shifted_colormap.shifted_colormap(cmap, min_val, max_val, name) → Colormap[source]

Function to offset the “center” of a colormap.

Useful for data with a negative min and positive max and you want the middle of the colormap’s dynamic range to be at zero.

diff --git a/api/nbnode.simulation.html b/api/nbnode.simulation.html index da30ed1..f30dd9b 100644 --- a/api/nbnode.simulation.html +++ b/api/nbnode.simulation.html @@ -5,10 +5,10 @@ - nbnode.simulation package — nbnode 0.0.post1.dev1 documentation + nbnode.simulation package — nbnode 0.0.post1 documentation - + @@ -41,12 +41,12 @@

Submodules

nbnode.simulation.FlowSimulationTree module

-class nbnode.simulation.FlowSimulationTree.BaseFlowSimulationTree(rootnode: NBNode, data_cellgroup_col: str = 'sample_name', node_percentages: DataFrame | None = None, seed: int = 12987, include_features: List[str] = 'dataset_melanoma', verbose: bool = False)[source]
+class nbnode.simulation.FlowSimulationTree.BaseFlowSimulationTree(rootnode: NBNode, data_cellgroup_col: str = 'sample_name', node_percentages: DataFrame | None = None, seed: int = 12987, include_features: List[str] = 'dataset_melanoma', verbose: bool = False)[source]

Bases: object

Base class for flow simulation.

-estimate_cell_distributions(nodes: List[NBNode]) → Dict[str, Dict[Literal['mu', 'cov'], DataFrame]][source]
+estimate_cell_distributions(nodes: List[NBNode]) → Dict[str, Dict[Literal['mu', 'cov'], DataFrame]][source]

Estimate the distribution of cells in each node.

If no distribution can be estimated (less than 2 cells), @@ -178,7 +178,7 @@

Submodules
-ncells_from_percentages(percentages: DataFrame, n_cells: int) → List[int][source]
+ncells_from_percentages(percentages: DataFrame, n_cells: int) → List[int][source]

‘Sample’ the number of cells according to the random percentages

Parameters:
@@ -234,7 +234,7 @@

Submodules
-sample(n_cells: int = 10000, return_sampled_cell_numbers: bool = False, use_only_diagonal_covmat: bool = True, **population_parameters) → Tuple[DataFrame, Series] | DataFrame[source]
+sample(n_cells: int = 10000, return_sampled_cell_numbers: bool = False, use_only_diagonal_covmat: bool = True, **population_parameters) → Tuple[DataFrame, Series] | DataFrame[source]

Sample cells from the tree.

Parameters:
@@ -261,7 +261,7 @@

Submodules
-sample_populations(n_cells: int = 10000, **population_parameters) → Series[source]
+sample_populations(n_cells: int = 10000, **population_parameters) → Series[source]

Generate number of cells according to leaf node population distributions.

Parameters:
@@ -291,12 +291,12 @@

Submodules
-class nbnode.simulation.FlowSimulationTree.FlowSimulationTreeDirichlet(rootnode: NBNode, data_cellgroup_col: str = 'sample_name', node_percentages: DataFrame | None = None, seed: int = 12987, include_features='dataset_melanoma', verbose: bool = False)[source]
+class nbnode.simulation.FlowSimulationTree.FlowSimulationTreeDirichlet(rootnode: NBNode, data_cellgroup_col: str = 'sample_name', node_percentages: DataFrame | None = None, seed: int = 12987, include_features='dataset_melanoma', verbose: bool = False)[source]

Bases: BaseFlowSimulationTree

Simulate a tree of cell populations using the Dirichlet distribution.

-property alpha_all: Series
+property alpha_all: Series

The alpha parameter of the Dirichlet distribution for all populations

Concentration parameters “alpha” of the Dirichlet distribution. The alpha parameter is a vector of positive values, where each value @@ -323,7 +323,7 @@

Submodules
-generate_populations(population_parameters, n_cells: int, *args, **kwargs) → DataFrame[source]
+generate_populations(population_parameters, n_cells: int, *args, **kwargs) → DataFrame[source]

Generate a population of cells using the Dirichlet distribution.

Parameters:
@@ -350,7 +350,7 @@

Submodules
-property mean_leafs: Series
+property mean_leafs: Series

Mean from dirichlet distribution

Estimating a Dirichlet distribution Thomas P. Minka @@ -551,7 +551,7 @@

Submodules
-sample() → Tuple[DataFrame, Dict[str, Any], List[DataFrame]][source]
+sample() → Tuple[DataFrame, Dict[str, Any], List[DataFrame]][source]

A method to sample with a relative change in a population mean.

See the __init__ method for the description of the arguments.

@@ -573,7 +573,7 @@

Submodules
-sample_customize(n_samples=None, n_cells=None, change_pop_mean_proportional=None, use_only_diagonal_covmat=None, verbose=None, seed_sample_0=None, save_dir=None, _only_return_sampled_cell_numbers=None, save_changed_parameters=False) → Tuple[DataFrame, Dict[str, Any], List[DataFrame]][source]
+sample_customize(n_samples=None, n_cells=None, change_pop_mean_proportional=None, use_only_diagonal_covmat=None, verbose=None, seed_sample_0=None, save_dir=None, _only_return_sampled_cell_numbers=None, save_changed_parameters=False) → Tuple[DataFrame, Dict[str, Any], List[DataFrame]][source]

A customizable method to sample with a relative change in a population mean.

See the __init__ method for the description of the arguments. In contrast to .sample(), this method allows to change each parameter @@ -604,7 +604,7 @@

Submodules

nbnode.simulation.sim_proportional module

-nbnode.simulation.sim_proportional.sim_proportional(flowsim: FlowSimulationTreeDirichlet, n_samples=100, n_cells=25000, use_only_diagonal_covmat=True, change_pop_mean_proportional={'/AllCells/CD4+/CD8-/Tem': 1}, save_dir='sim/intraassay/sim00_baseline', seed_sample_0=129873, verbose=False, only_return_sampled_cell_numbers=False) → Tuple[DataFrame, Dict[str, Any], List[DataFrame]][source]
+nbnode.simulation.sim_proportional.sim_proportional(flowsim: FlowSimulationTreeDirichlet, n_samples=100, n_cells=25000, use_only_diagonal_covmat=True, change_pop_mean_proportional={'/AllCells/CD4+/CD8-/Tem': 1}, save_dir='sim/intraassay/sim00_baseline', seed_sample_0=129873, verbose=False, only_return_sampled_cell_numbers=False) → Tuple[DataFrame, Dict[str, Any], List[DataFrame]][source]

This function simulates new cells (n_cells) for n_samples samples according to the given flow simulation flowsim.

@@ -669,7 +669,7 @@

Submodules

nbnode.simulation.sim_target module

-nbnode.simulation.sim_target.sim_target(flowsim: FlowSimulationTreeDirichlet, change_pop_mean_target: List[Dict[str, float]] = [{'/AllCells/CD4+/CD8-/Tem': 0.05}], n_cells=25000, use_only_diagonal_covmat=True, save_dir='sim/intraassay/sim00_target', sample_name=None, seed_sample_0=129873, verbose=False, only_return_sampled_cell_numbers=False, save_changed_parameters=False) → Tuple[DataFrame, Dict[str, Any], List[DataFrame]][source]
+nbnode.simulation.sim_target.sim_target(flowsim: FlowSimulationTreeDirichlet, change_pop_mean_target: List[Dict[str, float]] = [{'/AllCells/CD4+/CD8-/Tem': 0.05}], n_cells=25000, use_only_diagonal_covmat=True, save_dir='sim/intraassay/sim00_target', sample_name=None, seed_sample_0=129873, verbose=False, only_return_sampled_cell_numbers=False, save_changed_parameters=False) → Tuple[DataFrame, Dict[str, Any], List[DataFrame]][source]

This function simulates new cells (n_cells) for n_samples samples according to the given flow simulation flowsim.

diff --git a/api/nbnode.specific_analyses.html b/api/nbnode.specific_analyses.html index dad9752..9c3b896 100644 --- a/api/nbnode.specific_analyses.html +++ b/api/nbnode.specific_analyses.html @@ -5,10 +5,10 @@ - nbnode.specific_analyses package — nbnode 0.0.post1.dev1 documentation + nbnode.specific_analyses package — nbnode 0.0.post1 documentation - + diff --git a/api/nbnode.specific_analyses.intraassay.html b/api/nbnode.specific_analyses.intraassay.html index 2bbdde8..2762664 100644 --- a/api/nbnode.specific_analyses.intraassay.html +++ b/api/nbnode.specific_analyses.intraassay.html @@ -5,10 +5,10 @@ - nbnode.specific_analyses.intraassay package — nbnode 0.0.post1.dev1 documentation + nbnode.specific_analyses.intraassay package — nbnode 0.0.post1 documentation - + @@ -69,7 +69,7 @@

Submodules

nbnode.specific_analyses.intraassay.gate_init module

-nbnode.specific_analyses.intraassay.gate_init.gate_init(sample_list: List[str] | None = None) → Tuple[NBNode, DataFrame, FlowSimulationTreeDirichlet][source]
+nbnode.specific_analyses.intraassay.gate_init.gate_init(sample_list: List[str] | None = None) → Tuple[NBNode, DataFrame, FlowSimulationTreeDirichlet][source]

Gate the intraassay samples and generate the Dirichlet-based simulation.

Parameters:
diff --git a/api/nbnode.specific_analyses.intraassay.sims.html b/api/nbnode.specific_analyses.intraassay.sims.html index dac5ca6..09e6a1b 100644 --- a/api/nbnode.specific_analyses.intraassay.sims.html +++ b/api/nbnode.specific_analyses.intraassay.sims.html @@ -5,10 +5,10 @@ - nbnode.specific_analyses.intraassay.sims package — nbnode 0.0.post1.dev1 documentation + nbnode.specific_analyses.intraassay.sims package — nbnode 0.0.post1 documentation - + diff --git a/api/nbnode.testutil.html b/api/nbnode.testutil.html index 771aaac..60e04f9 100644 --- a/api/nbnode.testutil.html +++ b/api/nbnode.testutil.html @@ -5,10 +5,10 @@ - nbnode.testutil package — nbnode 0.0.post1.dev1 documentation + nbnode.testutil package — nbnode 0.0.post1 documentation - + diff --git a/api/nbnode.utils.html b/api/nbnode.utils.html index a468da2..a65d895 100644 --- a/api/nbnode.utils.html +++ b/api/nbnode.utils.html @@ -5,10 +5,10 @@ - nbnode.utils package — nbnode 0.0.post1.dev1 documentation + nbnode.utils package — nbnode 0.0.post1 documentation - + @@ -40,7 +40,7 @@

Submodules

nbnode.utils.merge_leaf_nodes module

-nbnode.utils.merge_leaf_nodes.merge_leaf_nodes(leaf_nodes_df: DataFrame, intermediate_node: str) → float[source]
+nbnode.utils.merge_leaf_nodes.merge_leaf_nodes(leaf_nodes_df: DataFrame, intermediate_node: str) → float[source]

Merge leaf node dataframe into intermediate node.

Parameters:
diff --git a/authors.html b/authors.html index 00edfb7..afbac66 100644 --- a/authors.html +++ b/authors.html @@ -5,10 +5,10 @@ - Contributors — nbnode 0.0.post1.dev1 documentation + Contributors — nbnode 0.0.post1 documentation - + diff --git a/changelog.html b/changelog.html index 127316e..779bfca 100644 --- a/changelog.html +++ b/changelog.html @@ -5,10 +5,10 @@ - Changelog — nbnode 0.0.post1.dev1 documentation + Changelog — nbnode 0.0.post1 documentation - + diff --git a/contributing.html b/contributing.html index f5b94c5..6295a90 100644 --- a/contributing.html +++ b/contributing.html @@ -5,10 +5,10 @@ - Contributing — nbnode 0.0.post1.dev1 documentation + Contributing — nbnode 0.0.post1 documentation - + diff --git a/genindex.html b/genindex.html index f90a0e1..0728c1c 100644 --- a/genindex.html +++ b/genindex.html @@ -4,10 +4,10 @@ - Index — nbnode 0.0.post1.dev1 documentation + Index — nbnode 0.0.post1 documentation - + diff --git a/index.html b/index.html index 6cf0a3e..31947ac 100644 --- a/index.html +++ b/index.html @@ -5,10 +5,10 @@ - NBNode Documentation — nbnode 0.0.post1.dev1 documentation + NBNode Documentation — nbnode 0.0.post1 documentation - + diff --git a/license.html b/license.html index e67193d..885c6a0 100644 --- a/license.html +++ b/license.html @@ -5,10 +5,10 @@ - License — nbnode 0.0.post1.dev1 documentation + License — nbnode 0.0.post1 documentation - + diff --git a/notebooks.html b/notebooks.html index 84aa375..3a0c78c 100644 --- a/notebooks.html +++ b/notebooks.html @@ -5,10 +5,10 @@ - Tutorials — nbnode 0.0.post1.dev1 documentation + Tutorials — nbnode 0.0.post1 documentation - + diff --git a/notebooks/nbnode-01.html b/notebooks/nbnode-01.html index 1be0368..7cc1bb6 100644 --- a/notebooks/nbnode-01.html +++ b/notebooks/nbnode-01.html @@ -5,11 +5,11 @@ - Base Non-binary node functionality — nbnode 0.0.post1.dev1 documentation + Base Non-binary node functionality — nbnode 0.0.post1 documentation - + diff --git a/notebooks/nbnode-02.html b/notebooks/nbnode-02.html index 2ec985f..7605781 100644 --- a/notebooks/nbnode-02.html +++ b/notebooks/nbnode-02.html @@ -5,11 +5,11 @@ - Part predictions and unfitting data — nbnode 0.0.post1.dev1 documentation + Part predictions and unfitting data — nbnode 0.0.post1 documentation - + diff --git a/notebooks/nbnode-03.html b/notebooks/nbnode-03.html index 1dda4d2..a95e10c 100644 --- a/notebooks/nbnode-03.html +++ b/notebooks/nbnode-03.html @@ -5,11 +5,11 @@ - Counting and math — nbnode 0.0.post1.dev1 documentation + Counting and math — nbnode 0.0.post1 documentation - + diff --git a/notebooks/nbnode-04.html b/notebooks/nbnode-04.html index 66af617..3069670 100644 --- a/notebooks/nbnode-04.html +++ b/notebooks/nbnode-04.html @@ -5,11 +5,11 @@ - Advanced predictions, data and plotting — nbnode 0.0.post1.dev1 documentation + Advanced predictions, data and plotting — nbnode 0.0.post1 documentation - + diff --git a/notebooks/nbnode-05_sim.html b/notebooks/nbnode-05_sim.html index 9278190..963c988 100644 --- a/notebooks/nbnode-05_sim.html +++ b/notebooks/nbnode-05_sim.html @@ -5,11 +5,11 @@ - Flow cytometry simulation. — nbnode 0.0.post1.dev1 documentation + Flow cytometry simulation. — nbnode 0.0.post1 documentation - + diff --git a/objects.inv b/objects.inv index f237dbf172e5e1076c7b77ea3fbb34ed6abc536c..a1ed37c9f5f46365b68bcae2c62681a9f5f51678 100644 GIT binary patch delta 10 RcmcbmbX94B^F|LLK>!)n1LFVy delta 15 WcmcbrbW3T1GmBnIYS~67VL<>en*~n* diff --git a/py-modindex.html b/py-modindex.html index efef765..5664c8b 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -4,10 +4,10 @@ - Python Module Index — nbnode 0.0.post1.dev1 documentation + Python Module Index — nbnode 0.0.post1 documentation - + diff --git a/readme.html b/readme.html index d8b58aa..77cdd40 100644 --- a/readme.html +++ b/readme.html @@ -5,10 +5,10 @@ - NBNode — nbnode 0.0.post1.dev1 documentation + NBNode — nbnode 0.0.post1 documentation - + diff --git a/search.html b/search.html index 76deb26..0b89e67 100644 --- a/search.html +++ b/search.html @@ -4,11 +4,11 @@ - Search — nbnode 0.0.post1.dev1 documentation + Search — nbnode 0.0.post1 documentation - +