cellrank.estimators.GPCCA¶
 class cellrank.estimators.GPCCA(object, **kwargs)[source]¶
Generalized Perron Cluster Cluster Analysis (GPCCA) [Reuter et al., 2019, Reuter et al., 2018].
See also
See Computing Initial and Terminal States on how to compute the
initial
andterminal
states.See Estimating Fate Probabilities and Driver Genes on how to compute the
fate_probabilities
andlineage_drivers
.
This is our main and recommended estimator implemented in pyGPCCA . Use it to compute macrostates, automatically and semiautomatically classify these as initial, intermediate and terminal states, compute fate probabilities towards macrostates, uncover driver genes, and much more. To compute and classify macrostates, we run the GPCCA algorithm under the hood, which returns a soft assignment of cells to macrostates, as well as a coarsegrained transition matrix among the set of macrostates [Reuter et al., 2019, Reuter et al., 2018]. This estimator allows you to inject prior knowledge where available to guide the identification of initial, intermediate and terminal states.
 Parameters:
object (
Union
[str
,bool
,ndarray
,spmatrix
,AnnData
,KernelExpression
]) –Can be one of the following types:
AnnData
 annotated data object.KernelExpression
 kernel expression.str
 key inobsp
where the transition matrix is stored andadata
must be provided in this case.bool
 directionality of the transition matrix that will be used to infer its storage location. IfNone
, the directionality will be determined automatically andadata
must be provided in this case.
kwargs (
Any
) – Keyword arguments for thePrecomputedKernel
.
Attributes table¶
Mean and variance of the time until absorption. 

Annotated data object. 

Direction of the 

Coarsegrained transition matrix. 

Coarsegrained initial distribution. 

Coarsegrained stationary distribution. 

Eigendecomposition of the 

Fate probabilities. 

Categorical annotation of initial states. 

Initial states memberships. 

Probability to be an initial state. 

Underlying kernel expression. 

Potential lineage drivers. 

Macrostates of the transition matrix. 

Macrostate memberships. 

Estimator parameters. 

Priming degree. 

Schur matrix. 

Real Schur vectors of the transition matrix. 

Shape of the kernel. 

Categorical annotation of terminal states. 

Terminal states memberships. 

Probability to be a terminal state. 

Transition matrix of the 
Methods table¶

Compute the mean time to absorption and optionally its variance. 

Compute eigendecomposition of the 

Compute fate probabilities. 

Compute driver genes per lineage. 

Compute the degree of lineage priming. 

Compute the macrostates. 

Compute the Schur decomposition. 

Return a copy of self. 

Prepare self for terminal states prediction. 

Deserialize self from 

Plot the coarsegrained transition matrix. 

Plot fate probabilities. 

Plot lineage drivers. 

Show scatter plot of genecorrelations between two lineages. 

Plot histogram of macrostates over categorical annotations. 

Plot macrostates on an embedding or along pseudotime. 

Plot the Schur matrix. 

Plot the top eigenvalues in a real or a complex plane. 

Plot terminal state identificiation (TSI). 

Alias for 

Compute initial states from macrostates using 

Automatically select terminal states from macrostates. 

Deserialize self from a file. 

Rename the 

Rename the 

Set the 

Set the 

Serialize self to 

Compute terminal state identification (TSI) score. 

Serialize self to a file using 
Attributes¶
absorption_times¶
 GPCCA.absorption_times¶
Mean and variance of the time until absorption.
Related to conditional mean first passage times. Corresponds to the expectation of the time until absorption, depending on initialization, and the variance.
adata¶
 GPCCA.adata¶
Annotated data object.
backward¶
coarse_T¶
 GPCCA.coarse_T¶
Coarsegrained transition matrix.
coarse_initial_distribution¶
 GPCCA.coarse_initial_distribution¶
Coarsegrained initial distribution.
coarse_stationary_distribution¶
 GPCCA.coarse_stationary_distribution¶
Coarsegrained stationary distribution.
eigendecomposition¶
 GPCCA.eigendecomposition¶
Eigendecomposition of the
transition_matrix
.For nonsymmetric real matrices, left and right eigenvectors will in general be different and complex. We compute both left and right eigenvectors.
 Returns:
A dictionary with the following keys:
'D'
 the eigenvalues.'eigengap'
 the eigengap.'params'
 parameters used for the computation.'V_l'
 left eigenvectors (optional).'V_r'
 right eigenvectors (optional).'stationary_dist'
 stationary distribution of thetransition_matrix
, if present.
fate_probabilities¶
 GPCCA.fate_probabilities¶
Fate probabilities.
Informally, given a (finite, discrete) Markov chain with a set of transient states \(T\) and a set of absorbing states \(A\), the absorption probability for cell \(i\) from \(T\) to reach cell \(j\) from \(R\) is the probability that a random walk initialized in \(i\) will reach absorbing state \(j\).
In our context, states correspond to cells, in particular, absorbing states correspond to cells in
terminal_states
.
initial_states¶
 GPCCA.initial_states¶
Categorical annotation of initial states.
By default, all transient cells will be labeled as NaN.
initial_states_memberships¶
 GPCCA.initial_states_memberships¶
Initial states memberships.
Soft assignment of cells to initial states.
initial_states_probabilities¶
 GPCCA.initial_states_probabilities¶
Probability to be an initial state.
kernel¶
 GPCCA.kernel¶
Underlying kernel expression.
lineage_drivers¶
 GPCCA.lineage_drivers¶
Potential lineage drivers.
Computes Pearson correlation of each gene with fate probabilities for every terminal state. High Pearson correlation indicates potential lineage drivers. Also computes pvalues and confidence intervals.
 Returns:
Dataframe of shape
(n_genes, n_lineages * 5)
containing the following columns, one for each lineage:
macrostates¶
 GPCCA.macrostates¶
Macrostates of the transition matrix.
macrostates_memberships¶
 GPCCA.macrostates_memberships¶
Macrostate memberships.
Soft assignment of microstates (cells) to macrostates.
params¶
 GPCCA.params¶
Estimator parameters.
priming_degree¶
 GPCCA.priming_degree¶
Priming degree.
Given a cell \(i\) and a set of terminal states, this quantifies how committed vs. naive cell \(i\) is, i.e. its degree of pluripotency. Low values correspond to naive cells (high degree of pluripotency), high values correspond to committed cells (low degree of pluripotency).
schur_matrix¶
 GPCCA.schur_matrix¶
Schur matrix.
The real Schur decomposition is a generalization of the Eigendecomposition and can be computed for any realvalued, square matrix \(A\). It is given by \(A = Q R Q^T\), where \(Q\) contains the real Schur vectors and \(R\) is the Schur matrix. \(Q\) is orthogonal and \(R\) is quasiupper triangular with 1x1 and 2x2 blocks on the diagonal.
If PETSc and SLEPc are installed, only the leading Schur vectors are computed.
schur_vectors¶
 GPCCA.schur_vectors¶
Real Schur vectors of the transition matrix.
The real Schur decomposition is a generalization of the Eigendecomposition and can be computed for any realvalued, square matrix \(A\). It is given by \(A = Q R Q^T\), where \(Q\) contains the real Schur vectors and \(R\) is the Schur matrix. \(Q\) is orthogonal and \(R\) is quasiupper triangular with 1x1 and 2x2 blocks on the diagonal.
If PETSc and SLEPc are installed, only the leading Schur vectors are computed.
shape¶
 GPCCA.shape¶
Shape of the kernel.
terminal_states¶
 GPCCA.terminal_states¶
Categorical annotation of terminal states.
By default, all transient cells will be labeled as NaN.
terminal_states_memberships¶
 GPCCA.terminal_states_memberships¶
Terminal states memberships.
Soft assignment of cells to terminal states.
terminal_states_probabilities¶
 GPCCA.terminal_states_probabilities¶
Probability to be a terminal state.
transition_matrix¶
Methods¶
compute_absorption_times¶
 GPCCA.compute_absorption_times(keys=None, calculate_variance=False, solver='gmres', use_petsc=True, n_jobs=None, backend='loky', show_progress_bar=None, tol=1e06, preconditioner=None)¶
Compute the mean time to absorption and optionally its variance.
 Parameters:
keys (
Optional
[Sequence
[str
]]) – Terminal states for which to compute the fate probabilities. IfNone
, use all states defined interminal_states
.calculate_variance (
bool
) – Whether to calculate the variance.solver (
Union
[str
,Literal
['direct'
,'gmres'
,'lgmres'
,'bicgstab'
,'gcrotmk'
]]) –Solver to use for the linear problem. Options are
'direct'
,'gmres'
,'lgmres'
,'bicgstab'
or'gcrotmk'
whenuse_petsc = False
.Information on the
scipy
iterative solvers can be found inscipy.sparse.linalg
or for thepetsc
solvers here.use_petsc (
bool
) – Whether to use solvers frompetsc4py
orscipy
. Recommended for large problems. If no installation is found, defaults togmres()
.n_jobs (
Optional
[int
]) – Number of parallel jobs to use when using an iterative solver.backend (
Literal
['loky'
,'multiprocessing'
,'threading'
]) – Which backend to use for multiprocessing. SeeParallel
for valid options.show_progress_bar (
Optional
[bool
]) – Whether to show progress bar. Only used whensolver != 'direct'
.tol (
float
) – Convergence tolerance for the iterative solver. The default is fine for most cases, only consider decreasing this for severely illconditioned matrices.preconditioner (
Optional
[str
]) – Preconditioner to use, only available whenuse_petsc = True
. For valid options, see here. We recommend the'ilu'
preconditioner for badly conditioned problems.self (FateProbsProtocol)
 Return type:
 Returns:
: Nothing, just updates the following fields:
absorption_times
 Mean and variance of the time until absorption.
compute_eigendecomposition¶
 GPCCA.compute_eigendecomposition(k=20, which='LR', alpha=1.0, only_evals=False, ncv=None)¶
Compute eigendecomposition of the
transition_matrix
.Uses a sparse implementation, if possible, and only computes the top \(k\) eigenvectors to speed up the computation. Computes both left and right eigenvectors.
 Parameters:
k (
int
) – Number of eigenvectors or eigenvalues to compute.which (
Literal
['LR'
,'LM'
]) –How to sort the eigenvalues. Valid option are:
'LR'
 the largest real part.'LM'
 the largest magnitude.
alpha (
float
) – Used to compute the eigengap.alpha
is the weight given to the deviation of an eigenvalue from one.only_evals (
bool
) – Whether to compute only eigenvalues.self (EigenProtocol)
 Return type:
EigenMixin
 Returns:
: Self and updates the following fields:
eigendecomposition
 Eigendecomposition of thetransition_matrix
.
compute_fate_probabilities¶
 GPCCA.compute_fate_probabilities(keys=None, solver='gmres', use_petsc=True, n_jobs=None, backend='loky', show_progress_bar=True, tol=1e06, preconditioner=None)¶
Compute fate probabilities.
For each cell, this computes the probability of being absorbed in any of the
terminal_states
. In particular, this corresponds to the probability that a random walk initialized in transient cell \(i\) will reach any cell from a fixed transient state before reaching a cell from any other transient state. Parameters:
keys (
Optional
[Sequence
[str
]]) – Terminal states for which to compute the fate probabilities. IfNone
, use all states defined interminal_states
.solver (
Union
[str
,Literal
['direct'
,'gmres'
,'lgmres'
,'bicgstab'
,'gcrotmk'
]]) –Solver to use for the linear problem. Options are
'direct'
,'gmres'
,'lgmres'
,'bicgstab'
or'gcrotmk'
whenuse_petsc = False
.Information on the
scipy
iterative solvers can be found inscipy.sparse.linalg
or for thepetsc
solvers here.use_petsc (
bool
) – Whether to use solvers frompetsc4py
orscipy
. Recommended for large problems. If no installation is found, defaults togmres()
.n_jobs (
Optional
[int
]) – Number of parallel jobs to use when using an iterative solver.backend (
Literal
['loky'
,'multiprocessing'
,'threading'
]) – Which backend to use for multiprocessing. SeeParallel
for valid options.show_progress_bar (
bool
) – Whether to show progress bar. Only used whensolver != 'direct'
.tol (
float
) – Convergence tolerance for the iterative solver. The default is fine for most cases, only consider decreasing this for severely illconditioned matrices.preconditioner (
Optional
[str
]) – Preconditioner to use, only available whenuse_petsc = True
. For valid options, see here. We recommend the'ilu'
preconditioner for badly conditioned problems.self (FateProbsProtocol)
 Return type:
 Returns:
: Nothing, just updates the following fields:
fate_probabilities
 Fate probabilities.
compute_lineage_drivers¶
 GPCCA.compute_lineage_drivers(lineages=None, method='fisher', cluster_key=None, clusters=None, layer=None, use_raw=False, confidence_level=0.95, n_perms=1000, seed=None, **kwargs)¶
Compute driver genes per lineage.
Correlates gene expression with lineage probabilities, for a given lineage and set of clusters. Often, it makes sense to restrict this to a set of clusters which are relevant for the specified lineages.
 Parameters:
lineages (
Union
[str
,Sequence
,None
]) – Lineage names fromfate_probabilities
. IfNone
, use all lineages.method (
Literal
['fisher'
,'perm_test'
]) –Mode to use when calculating pvalues and confidence intervals. Valid options are:
'fisher'
 Fisher transformation [Fisher, 1921].'perm_test'
 permutation test.
cluster_key (
Optional
[str
]) – Key inobs
to obtain cluster annotations. These are considered forclusters
.clusters (
Union
[str
,Sequence
,None
]) – Restrict the correlations to these clusters.layer (
Optional
[str
]) – Key fromlayers
from which to get the expression. IfNone
or ‘X’, useX
.use_raw (
bool
) – Whether to useraw
to correlate gene expression.confidence_level (
float
) – Confidence level for the confidence interval calculation. Must be in interval \([0, 1]\).n_perms (
int
) – Number of permutations to use whenmethod = 'perm_test'
.seed (
Optional
[int
]) – Random seed whenmethod = 'perm_test'
.show_progress_bar – Whether to show a progress bar. Disabling it may slightly improve performance.
n_jobs – Number of parallel jobs. If 1, use all available cores. If
None
or 1, the execution is sequential.backend – Which backend to use for parallelization. See
Parallel
for valid options.kwargs (
Any
) – Keyword for the correlation test.self (LinDriversProtocol)
 Return type:
 Returns:
: Dataframe of shape
(n_genes, n_lineages * 5)
containing the following columns, one for each lineage: Also updates the following field:lineage_drivers
 the samepandas.DataFrame
as described above.
compute_lineage_priming¶
 GPCCA.compute_lineage_priming(method='kl_divergence', early_cells=None)¶
Compute the degree of lineage priming.
It returns a score in \([0, 1]\) where \(0\) stands for naive and \(1\) stands for committed.
 Parameters:
method (
Literal
['kl_divergence'
,'entropy'
]) –The method used to compute the degree of lineage priming. Valid options are:
'kl_divergence'
 as in [Velten et al., 2017], computes KLdivergence between the fate probabilities of a cell and the average fate probabilities. Computation of average fate probabilities can be restricted to a set of userdefinedearly_cells
.'entropy'
 as in [Setty et al., 2019], computes entropy over a cell’s fate probabilities.
early_cells (
Union
[Mapping
[str
,Sequence
[str
]],Sequence
[str
],None
]) – Cell IDs or a mask marking early cells. IfNone
, use all cells. Only used whenmethod = 'kl_divergence'
. If adict
, the key specifies a cluster key inobs
and the values specify cluster labels containing early cells.self (FateProbsProtocol)
 Return type:
 Returns:
: Returns the priming degree and updates the following fields:
priming_degree
 Priming degree.
compute_macrostates¶
 GPCCA.compute_macrostates(n_states=None, n_cells=30, cluster_key=None, **kwargs)[source]¶
Compute the macrostates.
 Parameters:
n_states (
Union
[int
,Sequence
[int
],None
]) – Number of macrostates to compute. If aSequence
, use the minChi criterion [Reuter et al., 2018]. IfNone
, use the eigengap heuristic.n_cells (
Optional
[int
]) – Number of most likely cells from each macrostate to select.cluster_key (
Optional
[str
]) – If a key to cluster labels is given, names and colors of the states will be associated with the clusters.kwargs (
Any
) – Keyword arguments forcompute_schur()
.
 Return type:
 Returns:
: Returns self and updates the following fields:
macrostates
 Macrostates of the transition matrix.macrostates_memberships
 Macrostate memberships.coarse_T
 Coarsegrained transition matrix.coarse_initial_distribution
 Coarsegrained initial distribution.coarse_stationary_distribution
 Coarsegrained stationary distribution.schur_vectors
 Real Schur vectors of the transition matrix.schur_matrix
 Schur matrix.eigendecomposition
 Eigendecomposition of thetransition_matrix
.
compute_schur¶
 GPCCA.compute_schur(n_components=20, initial_distribution=None, method='krylov', which='LR', alpha=1.0, verbose=None)¶
Compute the Schur decomposition.
 Parameters:
n_components (
int
) – Number of Schur vectors to compute.initial_distribution (
Optional
[ndarray
]) – Input distribution over all cells. IfNone
, uniform distribution is used.method (
Literal
['krylov'
,'brandts'
]) –Method for calculating the Schur vectors. Valid options are:
'krylov'
 an iterative procedure that computes a partial, sorted Schur decomposition for large, sparse matrices.'brandts'
 full sorted Schur decomposition of a dense matrix.
For benefits of each method, see
GPCCA
.which (
Literal
['LR'
,'LM'
]) –How to sort the eigenvalues. Valid option are:
'LR'
 the largest real part.'LM'
 the largest magnitude.
alpha (
float
) – Used to compute the eigengap.alpha
is the weight given to the deviation of an eigenvalue from one.verbose (
Optional
[bool
]) – Whether to print extra information when computing the Schur decomposition. IfNone
, it’s disabled whenmethod = 'krylov'
.self (SchurProtocol)
 Return type:
SchurMixin
 Returns:
: Self and just updates the following fields:
schur_vectors
 Real Schur vectors of the transition matrix.schur_matrix
 Schur matrix.eigendecomposition
 Eigendecomposition of thetransition_matrix
.
copy¶
fit¶
 GPCCA.fit(n_states=None, n_cells=30, cluster_key=None, **kwargs)[source]¶
Prepare self for terminal states prediction.
 Parameters:
n_states (
Union
[int
,Sequence
[int
],None
]) – Number of macrostates to compute. If aSequence
, use the minChi criterion [Reuter et al., 2018]. IfNone
, use the eigengap heuristic.n_cells (
Optional
[int
]) – Number of most likely cells from each macrostate to select.cluster_key (
Optional
[str
]) – If a key to cluster labels is given, names and colors of the states will be associated with the clusters.kwargs (
Any
) – Keyword arguments forcompute_schur()
.
 Return type:
 Returns:
: Returns self and updates the following fields:
from_adata¶
plot_coarse_T¶
 GPCCA.plot_coarse_T(show_stationary_dist=True, show_initial_dist=False, order='stability', cmap='viridis', xtick_rotation=45, annotate=True, show_cbar=True, title=None, figsize=(8, 8), dpi=80, save=None, text_kwargs=mappingproxy({}), **kwargs)[source]¶
Plot the coarsegrained transition matrix.
 Parameters:
show_stationary_dist (
bool
) – Whether to show thecoarse_stationary_distribution
, if present.show_initial_dist (
bool
) – Whether to show thecoarse_initial_distribution
.order (
Optional
[Literal
['stability'
,'incoming'
,'outgoing'
,'stat_dist'
]]) –How to order the coarsegrained transition matrix. Valid options are:
'stability'
 order by the values on the diagonal.'incoming'
 order by the incoming mass, excluding the diagonal.'outgoing'
 order by the outgoing mass, excluding the diagonal.'stat_dist'
 order by coarse stationary distribution. If not present, use'stability'
.
cmap (
Union
[str
,ListedColormap
]) – Colormap to use.xtick_rotation (
float
) – Rotation of ticks on the xaxis.annotate (
bool
) – Whether to display the text on each cell.show_cbar (
bool
) – Whether to show the colorbar.dpi (
int
) – Dots per inch.save (
Union
[Path
,str
,None
]) – Filename where to save the plot.text_kwargs (
Mapping
[str
,Any
]) – Keyword arguments fortext()
.
 Return type:
 Returns:
: Nothing, just plots the figure. Optionally saves it based on
save
.
plot_fate_probabilities¶
 GPCCA.plot_fate_probabilities(states=None, color=None, mode='embedding', time_key=None, same_plot=True, title=None, cmap='viridis', **kwargs)¶
Plot fate probabilities.
 Parameters:
states (
Union
[str
,Sequence
[str
],None
]) – Subset of the macrostates to show. IfNone
, plot all macrostates.color (
Optional
[str
]) – Key inobs
oranndata.AnnData.var
used to color the observations.mode (
Literal
['embedding'
,'time'
]) – Whether to plot the probabilities in an embedding or along the pseudotime.time_key (
Optional
[str
]) – Key inobs
where pseudotime is stored. Only used whenmode = 'time'
.title (
Union
[str
,Sequence
[str
],None
]) – Title of the plot.same_plot (
bool
) – Whether to plot the data on the same plot or not. Only use whenmode = 'embedding'
. If True anddiscrete = False
,color
is ignored.cmap (
str
) – Colormap for continuous annotations.self (FateProbsProtocol)
 Return type:
 Returns:
: Nothing, just plots the figure. Optionally saves it based on
save
.
plot_lineage_drivers¶
 GPCCA.plot_lineage_drivers(lineage, n_genes=8, use_raw=False, ascending=False, ncols=None, title_fmt='{gene} qval={qval:.4e}', figsize=None, dpi=None, save=None, **kwargs)¶
Plot lineage drivers.
 Parameters:
lineage (
str
) – Lineage for which to plot the driver genes.n_genes (
int
) – Top most correlated genes to plot.ascending (
bool
) – Whether to sort the genes in ascending order.title_fmt (
str
) – Title format. Can include{gene}
,{pval}
,{qval}
or{corr}
, which will be substituted with the actual values.figsize (
Optional
[Tuple
[float
,float
]]) – Size of the figure.save (
Union
[Path
,str
,None
]) – Filename where to save the plot.self (LinDriversProtocol)
 Return type:
 Returns:
: Nothing, just plots the figure. Optionally saves it based on
save
.
plot_lineage_drivers_correlation¶
 GPCCA.plot_lineage_drivers_correlation(lineage_x, lineage_y, color=None, gene_sets=None, gene_sets_colors=None, use_raw=False, cmap='RdYlBu_r', fontsize=12, adjust_text=False, legend_loc='best', figsize=(4, 4), dpi=None, save=None, show=True, **kwargs)¶
Show scatter plot of genecorrelations between two lineages.
Optionally, a
dict
of gene names can be passed to highlight in the plot. Parameters:
lineage_x (
str
) – Name of the lineage on the xaxis.lineage_y (
str
) – Name of the lineage on the yaxis.color (
Optional
[str
]) – Key invar
orvarm
, preferring for the former.gene_sets (
Optional
[Dict
[str
,Sequence
[str
]]]) – Gene sets annotations of the form{'gene_set_name': ['gene_1', 'gene_2'], ...}
.gene_sets_colors (
Optional
[Sequence
[str
]]) – List of colors where each entry corresponds to a gene set fromgenes_sets
. If None and keys ingene_sets
correspond to lineage names, use the lineage colors. Otherwise, use default colors.cmap (
str
) – Colormap to use.fontsize (
int
) – Size of the text when plottinggene_sets
.adjust_text (
bool
) – Whether to automatically adjust text in order to reduce overlap.legend_loc (
Optional
[str
]) – Position of the legend. IfNone
, don’t show the legend. Only used whengene_sets != None
.figsize (
Optional
[Tuple
[float
,float
]]) – Size of the figure.save (
Union
[Path
,str
,None
]) – Filename where to save the plot.self (LinDriversProtocol)
 Return type:
 Returns:
: If
show = True
, nothing, just plots, otherwise returns the axes object. Optionally saves it based onsave
.
Notes
This plot is based on the following notebook by Maren Büttner.
plot_macrostate_composition¶
 GPCCA.plot_macrostate_composition(key, width=0.8, title=None, labelrot=45, legend_loc='upper right out', figsize=None, dpi=None, save=None, show=True)[source]¶
Plot histogram of macrostates over categorical annotations.
 Parameters:
adata – Annotated data object.
key (
str
) – Key fromobs
containing categorical annotations.width (
float
) – Bar width in \([0, 1]\).title (
Optional
[str
]) – Title of the figure. IfNone
, create one automatically.labelrot (
float
) – Rotation of labels on xaxis.legend_loc (
Optional
[str
]) – Position of the legend. IfNone
, don’t show the legend.figsize (
Optional
[Tuple
[float
,float
]]) – Size of the figure.save (
Union
[Path
,str
,None
]) – Filename where to save the plot.
 Return type:
 Returns:
: If
show = True
, nothing, just plots, otherwise returns the axes object. Optionally saves it based onsave
.
plot_macrostates¶
 GPCCA.plot_macrostates(which, states=None, color=None, discrete=True, mode='embedding', time_key='latent_time', same_plot=True, title=None, cmap='viridis', **kwargs)¶
Plot macrostates on an embedding or along pseudotime.
 Parameters:
which (
Literal
['all'
,'initial'
,'terminal'
]) –Which macrostates to plot. Valid options are:
'all'
 plot all macrostates.'initial'
 plot macrostates marked asinitial_states
.'terminal'
 plot macrostates marked asterminal_states
.
states (
Union
[str
,Sequence
[str
],None
]) – Subset of the macrostates to show. IfNone
, plot all macrostates.color (
Optional
[str
]) – Key inobs
orvar
used to color the observations.discrete (
bool
) – Whether to plot the data as continuous or discrete observations. If the data cannot be plotted as continuous observations, it will be plotted as discrete.mode (
Literal
['embedding'
,'time'
]) – Whether to plot the probabilities in an embedding or along the pseudotime.time_key (
str
) – Key inobs
where pseudotime is stored. Only used whenmode = 'time'
.title (
Union
[str
,Sequence
[str
],None
]) – Title of the plot.same_plot (
bool
) – Whether to plot the data on the same plot or not. Only use whenmode = 'embedding'
. If True anddiscrete = False
,color
is ignored.cmap (
str
) – Colormap for continuous annotations.
 Return type:
 Returns:
: Nothing, just plots the figure. Optionally saves it based on
save
.
plot_schur_matrix¶
 GPCCA.plot_schur_matrix(title='schur matrix', cmap='viridis', figsize=None, dpi=80, save=None, **kwargs)¶
Plot the Schur matrix.
 Parameters:
 Return type:
 Returns:
: Nothing, just plots the figure. Optionally saves it based on
save
.
plot_spectrum¶
 GPCCA.plot_spectrum(n=None, real_only=None, show_eigengap=True, show_all_xticks=True, legend_loc=None, title=None, marker='.', figsize=(5, 5), dpi=100, save=None, **kwargs)¶
Plot the top eigenvalues in a real or a complex plane.
 Parameters:
n (
Optional
[int
]) – Number of eigenvalues to show. IfNone
, show all that have been computed.real_only (
Optional
[bool
]) – Whether to plot only the real part of the spectrum. IfNone
, plot real spectrum if no complex eigenvalues are present.show_eigengap (
bool
) – Whenreal_only = True
, this determines whether to show the inferred eigengap as a dotted line.show_all_xticks (
bool
) – Whenreal_only = True
, this determines whether to show the indices of all eigenvalues on the xaxis.legend_loc (
Optional
[str
]) – Location parameter for the legend.marker (
str
) – Marker symbol used, valid options can be found inmarkers
.figsize (
Optional
[Tuple
[float
,float
]]) – Size of the figure.dpi (
int
) – Dots per inch.save (
Union
[Path
,str
,None
]) – Filename where to save the plot.
 Return type:
 Returns:
: Nothing, just plots the figure. Optionally saves it based on
save
.
plot_tsi¶
 GPCCA.plot_tsi(n_macrostates=None, x_offset=(0.2, 0.2), y_offset=(0.1, 0.1), figsize=(6, 4), dpi=None, save=None, **kwargs)[source]¶
Plot terminal state identificiation (TSI).
Requires computing TSI with
tsi()
first. Parameters:
 Return type:
 Returns:
: Plot TSI of the kernel and an optimal identification strategy.
predict¶
 GPCCA.predict(*args, **kwargs)[source]¶
Alias for
predict_terminal_states()
. Parameters:
 Return type:
 Returns:
: Same as
predict_terminal_states()
.
predict_initial_states¶
 GPCCA.predict_initial_states(n_states=1, n_cells=30, allow_overlap=False)[source]¶
Compute initial states from macrostates using
coarse_stationary_distribution
. Parameters:
 Return type:
 Returns:
: Returns self and updates the following fields:
initial_states
 Categorical annotation of initial states.initial_states_probabilities
 Probability to be an initial state.initial_states_memberships
 Initial states memberships.
predict_terminal_states¶
 GPCCA.predict_terminal_states(method='stability', n_cells=30, alpha=1, stability_threshold=0.96, n_states=None, allow_overlap=False)[source]¶
Automatically select terminal states from macrostates.
 Parameters:
method (
Literal
['stability'
,'top_n'
,'eigengap'
,'eigengap_coarse'
]) –How to select the terminal states. Valid option are:
'eigengap'
 select the number of states based on the eigengap oftransition_matrix
.'eigengap_coarse'
 select the number of states based on the eigengap of the diagonal ofcoarse_T
.'top_n'
 select topn_states
based on the probability of the diagonal ofcoarse_T
.'stability'
 select states which have a stability >=stability_threshold
. The stability is given by the diagonal elements ofcoarse_T
.
n_cells (
int
) – Number of most likely cells from each macrostate to select.alpha (
Optional
[float
]) – Weight given to the deviation of an eigenvalue from one. Only used whenmethod = 'eigengap'
ormethod = 'eigengap_coarse'
.stability_threshold (
float
) – Threshold used whenmethod = 'stability'
.n_states (
Optional
[int
]) – Number of states used whenmethod = 'top_n'
.allow_overlap (
bool
) – Whether to allow overlapping names between initial and terminal states.
 Return type:
 Returns:
: Returns self and updates the following fields:
terminal_states
 Categorical annotation of terminal states.terminal_states_probabilities
 Probability to be a terminal state.terminal_states_memberships
 Terminal states memberships.
read¶
 static GPCCA.read(fname, adata=None, copy=False)¶
Deserialize self from a file.
 Parameters:
fname (
Union
[str
,Path
]) – Path from which to read the object.adata (
Optional
[AnnData
]) –AnnData
object to assign to the saved object. Only used when the saved object hasadata
and it was saved without it.copy (
bool
) – Whether to copyadata
before assigning it. Ifadata
is a view, it is always copied.
 Return type:
IOMixin
 Returns:
: The deserialized object.
rename_initial_states¶
 GPCCA.rename_initial_states(old_new)¶
Rename the
initial_states
. Parameters:
old_new (
Dict
[str
,str
]) – Dictionary that maps old names to unique new names. Return type:
 Returns:
: Returns self and updates the following fields:
initial_states
 Categorical annotation of initial states.
rename_terminal_states¶
 GPCCA.rename_terminal_states(old_new)¶
Rename the
terminal_states
. Parameters:
old_new (
Dict
[str
,str
]) – Dictionary that maps old names to unique new names. Return type:
 Returns:
: Returns self and updates the following fields:
terminal_states
 Categorical annotation of terminal states.
set_initial_states¶
 GPCCA.set_initial_states(states=None, n_cells=30, allow_overlap=False, cluster_key=None, **kwargs)[source]¶
Set the
initial_states
. Parameters:
states (
Union
[str
,Sequence
[str
],Dict
[str
,Sequence
[str
]],Series
,None
]) –Which states to select. Valid options are:
str
,Sequence
 subset ofmacrostates
. Multiple states can be combined using','
, such as['Alpha, Beta', 'Epsilon']
.dict
 keys correspond to initial states and values to cell IDs inobs_names
.Series
 categorical series where each category corresponds to a macrostate. NaN values mark cells that should not be marked asinitial_states
.None
 select allmacrostates
.
n_cells (
int
) – Number of most likely cells from each macrostate to select.allow_overlap (
bool
) – Whether to allow overlapping names between initial and terminal states.cluster_key (
Optional
[str
]) – Key inobs
to associate names and colors withinitial_states
. Each state will be given the name and color corresponding to the cluster it mostly overlaps with. Only used whenstates
is adict
orSeries
.kwargs (
Any
) – Additional keyword arguments.
 Return type:
 Returns:
: Returns self and updates the following fields:
initial_states
 Categorical annotation of initial states.initial_states_probabilities
 Probability to be an initial state.initial_states_memberships
 Initial states memberships.
set_terminal_states¶
 GPCCA.set_terminal_states(states=None, n_cells=30, allow_overlap=False, cluster_key=None, **kwargs)[source]¶
Set the
terminal_states
. Parameters:
states (
Union
[str
,Sequence
[str
],Dict
[str
,Sequence
[str
]],Series
,None
]) –Which states to select. Valid options are:
str
,Sequence
 subset ofmacrostates
. Multiple states can be combined using','
, such as['Alpha, Beta', 'Epsilon']
.dict
 keys correspond to terminal states and values to cell IDs inobs_names
.Series
 categorical series where each category corresponds to a macrostate. NaN values mark cells that should not be marked asterminal_states
.None
 select allmacrostates
.
n_cells (
int
) – Number of most likely cells from each macrostate to select.allow_overlap (
bool
) – Whether to allow overlapping names between initial and terminal states.cluster_key (
Optional
[str
]) – Key inobs
to associate names and colors withterminal_states
. Each state will be given the name and color corresponding to the cluster it mostly overlaps with. Only used whenstates
is adict
orSeries
.kwargs (
Any
) – Additional keyword arguments.
 Return type:
 Returns:
: Returns self and updates the following fields:
terminal_states
 Categorical annotation of terminal states.terminal_states_probabilities
 Probability to be a terminal state.terminal_states_memberships
 Terminal states memberships.
to_adata¶
 GPCCA.to_adata(keep=('X', 'raw'), *, copy=True)¶
Serialize self to
Anndata
. Parameters:
keep (
Union
[Literal
['all'
],Sequence
[Literal
['X'
,'raw'
,'layers'
,'obs'
,'var'
,'obsm'
,'varm'
,'obsp'
,'varp'
,'uns'
]]]) –Which attributes to keep from the underlying
adata
. Valid options are:'all'
 keep all attributes specified in the signature.Sequence
 keep only subset of these attributes.dict
 the keys correspond the attribute names and values to a subset of keys which to keep from this attribute. If the values are specified either asTrue
or'all'
, everything from this attribute will be kept.
copy (
Union
[bool
,Sequence
[Literal
['X'
,'raw'
,'layers'
,'obs'
,'var'
,'obsm'
,'varm'
,'obsp'
,'varp'
,'uns'
]]]) – Whether to copy the data. Can be specified on perattribute basis. Useful for attributes that are arraylike.
 Return type:
 Returns:
: Annotated data object.