cellrank.estimators.CFLARE

class cellrank.estimators.CFLARE(*args, **kwargs)

Clustering and filtering of left and right eigenvectors (CFLARE).

This estimator computes initial and terminal states, as well as fate probabilities. It uses the left eigenvectors of the transition matrix to filter to a set of (approximately) recurrent cells and the right eigenvectors to cluster this set of cells into discrete groups. CFLARE exists mostly for legacy reasons, we recommend using the cellrank.estimators.GPCCA estimator, which is mathematically more principled.

Parameters:

• object –

  Can be one of the following types:

  • AnnData - annotated data object.

  • spmatrix, ndarray - row-normalized transition matrix.

  • KernelExpression - kernel expression.

  • str - key in obsp where the transition matrix is stored and adata must be provided in this case.

  • bool - directionality of the transition matrix that will be used to infer its storage location. If None, the directionality will be determined automatically and adata must be provided in this case.

• kwargs (Any) – Keyword arguments for the PrecomputedKernel.

• args (Any)

Attributes table

absorption_times	Mean and variance of the time until absorption.
adata	Annotated data object.
backward	Direction of the kernel.
eigendecomposition	Eigendecomposition of the transition_matrix.
fate_probabilities	Fate probabilities.
initial_states	Categorical annotation of initial states.
initial_states_probabilities	Probability to be an initial state.
kernel	Underlying kernel expression.
lineage_drivers	Potential lineage drivers.
params	Estimator parameters.
priming_degree	Priming degree.
shape	Shape of the kernel.
terminal_states	Categorical annotation of terminal states.
terminal_states_probabilities	Probability to be a terminal state.
transition_matrix	Transition matrix of the kernel.

Methods table

compute_absorption_times([keys, ...])	Compute the mean time to absorption and optionally its variance.
compute_eigendecomposition([k, which, ...])	Compute eigendecomposition of the transition_matrix.
compute_fate_probabilities([keys, solver, ...])	Compute fate probabilities.
compute_lineage_drivers([lineages, method, ...])	Compute driver genes per lineage.
compute_lineage_priming([method, early_cells])	Compute the degree of lineage priming.
copy(*[, deep])	Return a copy of self.
fit([k])	Prepare self for terminal states prediction.
from_adata(adata, obsp_key)	De-serialize self from AnnData.
plot_fate_probabilities([states, color, ...])	Plot fate probabilities.
plot_lineage_drivers(lineage[, n_genes, ...])	Plot lineage drivers.
plot_lineage_drivers_correlation(lineage_x, ...)	Show scatter plot of gene-correlations between two lineages.
plot_macrostates(which[, states, color, ...])	Plot macrostates on an embedding or along pseudotime.
plot_spectrum([n, real_only, show_eigengap, ...])	Plot the top eigenvalues in a real or a complex plane.
predict([use, percentile, method, ...])	Find approximate recurrent classes of the Markov chain.
read(fname[, adata, copy])	De-serialize self from a file.
rename_initial_states(old_new)	Rename the initial_states.
rename_terminal_states(old_new)	Rename the terminal_states.
set_initial_states(states[, cluster_key, ...])	Set the initial_states.
set_terminal_states(states[, cluster_key, ...])	Set the terminal_states.
to_adata([keep, copy])	Serialize self to Anndata.
write(fname[, write_adata])	Serialize self to a file using pickle.

Attributes

absorption_times

CFLARE.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

CFLARE.adata

Annotated data object.

backward

CFLARE.backward

Direction of the kernel.

eigendecomposition

CFLARE.eigendecomposition

Eigendecomposition of the transition_matrix.

For non-symmetric 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 the transition_matrix, if present.

fate_probabilities

CFLARE.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

CFLARE.initial_states

Categorical annotation of initial states.

By default, all transient cells will be labeled as NaN.

initial_states_probabilities

CFLARE.initial_states_probabilities

Probability to be an initial state.

kernel

CFLARE.kernel

Underlying kernel expression.

lineage_drivers

CFLARE.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 p-values and confidence intervals.

Returns:

Dataframe of shape (n_genes, n_lineages * 5) containing the following columns, one for each lineage:

params

CFLARE.params

Estimator parameters.

priming_degree

CFLARE.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).

shape

CFLARE.shape

Shape of the kernel.

terminal_states

CFLARE.terminal_states

Categorical annotation of terminal states.

By default, all transient cells will be labeled as NaN.

terminal_states_probabilities

CFLARE.terminal_states_probabilities

Probability to be a terminal state.

transition_matrix

CFLARE.transition_matrix

Transition matrix of the kernel.

Methods

compute_absorption_times

CFLARE.compute_absorption_times(keys=None, calculate_variance=False, solver='gmres', use_petsc=True, n_jobs=None, backend='loky', show_progress_bar=None, tol=1e-06, preconditioner=None)

Compute the mean time to absorption and optionally its variance.

Parameters:

• keys (Sequence[str] | None) – Terminal states for which to compute the fate probabilities. If None, use all states defined in terminal_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' when use_petsc = False.

  Information on the scipy iterative solvers can be found in scipy.sparse.linalg or for the petsc solvers here.

• use_petsc (bool) – Whether to use solvers from petsc4py or scipy. Recommended for large problems. If no installation is found, defaults to gmres().

• n_jobs (int | None) – Number of parallel jobs to use when using an iterative solver.

• backend (Literal['loky', 'multiprocessing', 'threading']) – Which backend to use for multiprocessing. See Parallel for valid options.

• show_progress_bar (bool | None) – Whether to show progress bar. Only used when solver != 'direct'.

• tol (float) – Convergence tolerance for the iterative solver. The default is fine for most cases, only consider decreasing this for severely ill-conditioned matrices.

• preconditioner (str | None) – Preconditioner to use, only available when use_petsc = True. For valid options, see here. We recommend the 'ilu' preconditioner for badly conditioned problems.

• check_sum_tol – Tolerance for checking whether fate probabilities sum to 1. Fate probabilities are computed by solving a linear system; this tolerance is used to verify the solution is valid. Increase the argument value if the solver converges but the check fails due to numerical precision.

• self (FateProbsProtocol)

Return type:

None

Returns:

: Nothing, just updates the following fields:

• absorption_times - Mean and variance of the time until absorption.

compute_eigendecomposition

CFLARE.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.

• ncv (int | None) – Number of Lanczos vectors generated.

• self (EigenProtocol)

Return type:

EigenMixin

Returns:

: Self and updates the following fields:

• eigendecomposition - Eigendecomposition of the transition_matrix.

compute_fate_probabilities

CFLARE.compute_fate_probabilities(keys=None, solver='gmres', use_petsc=True, n_jobs=None, backend='loky', show_progress_bar=True, tol=1e-06, preconditioner=None, check_sum_tol=0.001)

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 (Sequence[str] | None) – Terminal states for which to compute the fate probabilities. If None, use all states defined in terminal_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' when use_petsc = False.

  Information on the scipy iterative solvers can be found in scipy.sparse.linalg or for the petsc solvers here.

• use_petsc (bool) – Whether to use solvers from petsc4py or scipy. Recommended for large problems. If no installation is found, defaults to gmres().

• n_jobs (int | None) – Number of parallel jobs to use when using an iterative solver.

• backend (Literal['loky', 'multiprocessing', 'threading']) – Which backend to use for multiprocessing. See Parallel for valid options.

• show_progress_bar (bool) – Whether to show progress bar. Only used when solver != 'direct'.

• tol (float) – Convergence tolerance for the iterative solver. The default is fine for most cases, only consider decreasing this for severely ill-conditioned matrices.

• preconditioner (str | None) – Preconditioner to use, only available when use_petsc = True. For valid options, see here. We recommend the 'ilu' preconditioner for badly conditioned problems.

• check_sum_tol (float) – Tolerance for checking whether fate probabilities sum to 1. Fate probabilities are computed by solving a linear system; this tolerance is used to verify the solution is valid. Increase the argument value if the solver converges but the check fails due to numerical precision.

• self (FateProbsProtocol)

Return type:

None

Returns:

: Nothing, just updates the following fields:

• fate_probabilities - Fate probabilities.

compute_lineage_drivers

CFLARE.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, nan_policy='propagate', **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 (str | Sequence | None) – Lineage names from fate_probabilities. If None, use all lineages.

• method (Literal['fisher', 'perm_test']) –

  Mode to use when calculating p-values and confidence intervals. Valid options are:

  • 'fisher' - Fisher transformation [Fisher, 1921].

  • 'perm_test' - permutation test.

• cluster_key (str | None) – Key in obs to obtain cluster annotations. These are considered for clusters.

• clusters (str | Sequence | None) – Restrict the correlations to these clusters.

• layer (str | None) – Key from layers from which to get the expression. If None or ‘X’, use X.

• use_raw (bool) – Whether to use raw 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 when method = 'perm_test'.

• seed (int | None) – Random seed when method = 'perm_test'.

• nan_policy (Literal['propagate', 'omit']) –

  How to handle missing values (nan) in the expression data. Valid options are:

  • 'propagate' - missing values propagate to the result.

  • 'omit' - correlate each gene and lineage only over the cells where both are non-missing, akin to scipy.stats.pearsonr(). Only supported for dense expression data and method = 'fisher'.

• 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:

DataFrame

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 same pandas.DataFrame as described above.

compute_lineage_priming

CFLARE.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 KL-divergence between the fate probabilities of a cell and the average fate probabilities. Computation of average fate probabilities can be restricted to a set of user-defined early_cells.

  • 'entropy' - as in [Setty et al., 2019], computes entropy over a cell’s fate probabilities.

• early_cells (Mapping[str, Sequence[str]] | Sequence[str] | None) – Cell IDs or a mask marking early cells. If None, use all cells. Only used when method = 'kl_divergence'. If a dict, the key specifies a cluster key in obs and the values specify cluster labels containing early cells.

• self (FateProbsProtocol)

Return type:

Series

Returns:

: Returns the priming degree and updates the following fields:

• priming_degree - Priming degree.

copy

CFLARE.copy(*, deep=False)

Return a copy of self.

Parameters:

deep (bool) – Whether to return a deep copy or not. If True, this also copies the adata.

Return type:

BaseEstimator

Returns:

: A copy of self.

fit

CFLARE.fit(k=20, **kwargs)

Prepare self for terminal states prediction.

Deprecated since version 2.1: Will be removed in CellRank 3.0. Use compute_eigendecomposition() directly.

Parameters:

• k (int) – Number of eigenvectors to compute.

• kwargs (Any) – Keyword arguments for compute_eigendecomposition().

Return type:

TermStatesEstimator

Returns:

: Returns self and updates the following fields:

• eigendecomposition - Eigendecomposition of the transition_matrix.

from_adata

classmethod CFLARE.from_adata(adata, obsp_key)

De-serialize self from AnnData.

Parameters:

• adata (AnnData) – Annotated data object.

• obsp_key (str) – Key in obsp where the transition matrix is stored.

Return type:

BaseEstimator

Returns:

: The de-serialized object.

plot_fate_probabilities

CFLARE.plot_fate_probabilities(states=None, color=None, mode='embedding', time_key=None, basis='umap', same_plot=True, title=None, cmap='viridis', **kwargs)

Plot fate probabilities.

Parameters:

• states (str | Sequence[str] | None) – Subset of the macrostates to show. If None, plot all macrostates.

• color (str | None) – Key in obs or anndata.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 (str | None) – Key in obs where pseudotime is stored. Only used when mode = 'time'.

• basis (str) – Key in obsm for the embedding to use, e.g. 'umap' or 'tsne'.

• title (str | Sequence[str] | None) – Title of the plot.

• same_plot (bool) – Whether to plot the data on the same plot or not. Only use when mode = 'embedding'. If True and discrete = False, color is ignored.

• cmap (str) – Colormap for continuous annotations.

• kwargs (Any) – Keyword arguments for embedding().

• self (FateProbsProtocol)

Return type:

None

Returns:

: Nothing, just plots the figure. Optionally saves it based on save.

plot_lineage_drivers

CFLARE.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.

• use_raw (bool) – Whether to access data in raw or not.

• ascending (bool) – Whether to sort the genes in ascending order.

• ncols (int | None) – Number of columns.

• title_fmt (str) – Title format. Can include {gene}, {pval}, {qval} or {corr}, which will be substituted with the actual values.

• figsize (tuple[float, float] | None) – Size of the figure.

• dpi (int | None) – Dots per inch.

• save (str | Path | None) – Filename where to save the plot.

• kwargs (Any) – Keyword arguments for embedding().

• self (LinDriversProtocol)

Return type:

None

Returns:

: Nothing, just plots the figure. Optionally saves it based on save.

plot_lineage_drivers_correlation

CFLARE.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 gene-correlations 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 x-axis.

• lineage_y (str) – Name of the lineage on the y-axis.

• color (str | None) – Key in var or varm, preferring for the former.

• gene_sets (dict[str, Sequence[str]] | None) – Gene sets annotations of the form {'gene_set_name': ['gene_1', 'gene_2'], ...}.

• gene_sets_colors (Sequence[str] | None) – List of colors where each entry corresponds to a gene set from genes_sets. If None and keys in gene_sets correspond to lineage names, use the lineage colors. Otherwise, use default colors.

• use_raw (bool) – Whether to access raw or not.

• cmap (str) – Colormap to use.

• fontsize (int) – Size of the text when plotting gene_sets.

• adjust_text (bool) – Whether to automatically adjust text in order to reduce overlap.

• legend_loc (str | None) – Position of the legend. If None, don’t show the legend. Only used when gene_sets != None.

• figsize (tuple[float, float] | None) – Size of the figure.

• dpi (int | None) – Dots per inch.

• save (str | Path | None) – Filename where to save the plot.

• show (bool) – If False, return the Axes object.

• kwargs (Any) – Keyword arguments for scatter().

• self (LinDriversProtocol)

Return type:

Axes | None

Returns:

: If show = True, nothing, just plots, otherwise returns the axes object. Optionally saves it based on save.

Notes

This plot is based on the following notebook by Maren Büttner.

plot_macrostates

CFLARE.plot_macrostates(which, states=None, color=None, discrete=True, mode='embedding', time_key='latent_time', basis='umap', same_plot=True, title=None, cmap='viridis', **kwargs)

Plot macrostates on an embedding or along pseudotime.

Parameters:

• which (Literal['all', 'initial', 'terminal', 'initial_and_terminal']) –

  Which macrostates to plot. Valid options are:

  • 'all' - plot all macrostates.

  • 'initial' - plot macrostates marked as initial_states.

  • 'terminal' - plot macrostates marked as terminal_states.

  • 'initial_and_terminal' - plot both initial_states and terminal_states in one plot. States are renamed to 'initial: <name>' and 'terminal: <name>' to tell them apart.

• states (str | Sequence[str] | None) – Subset of the macrostates to show. If None, plot all macrostates.

• color (str | None) – Key in obs or var 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 in obs where pseudotime is stored. Only used when mode = 'time'.

• basis (str) – Key in obsm for the embedding to use, e.g. 'umap' or 'tsne'.

• title (str | Sequence[str] | None) – Title of the plot.

• same_plot (bool) – Whether to plot the data on the same plot or not. Only use when mode = 'embedding'. If True and discrete = False, color is ignored.

• cmap (str) – Colormap for continuous annotations.

• kwargs (Any) – Keyword arguments for embedding().

Return type:

None

Returns:

: Nothing, just plots the figure. Optionally saves it based on save.

plot_spectrum

CFLARE.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 (int | None) – Number of eigenvalues to show. If None, show all that have been computed.

• real_only (bool | None) – Whether to plot only the real part of the spectrum. If None, plot real spectrum if no complex eigenvalues are present.

• show_eigengap (bool) – When real_only = True, this determines whether to show the inferred eigengap as a dotted line.

• show_all_xticks (bool) – When real_only = True, this determines whether to show the indices of all eigenvalues on the x-axis.

• legend_loc (str | None) – Location parameter for the legend.

• title (str | None) – Title of the figure.

• marker (str) – Marker symbol used, valid options can be found in markers.

• figsize (tuple[float, float] | None) – Size of the figure.

• dpi (int) – Dots per inch.

• save (str | Path | None) – Filename where to save the plot.

• kwargs (Any) – Keyword arguments for scatter().

Return type:

None

Returns:

: Nothing, just plots the figure. Optionally saves it based on save.

predict

CFLARE.predict(use=None, percentile=98, method='leiden', cluster_key=None, n_clusters_kmeans=None, n_neighbors=20, resolution=0.1, n_matches_min=0, n_neighbors_filtering=15, basis=None, n_comps=5, scale=None)

Find approximate recurrent classes of the Markov chain.

Deprecated since version 2.1: Will be removed in CellRank 3.0. The entire CFLARE estimator is deprecated. Use cellrank.estimators.GPCCA instead.

Filter to obtain recurrent states from left eigenvectors. Cluster to obtain approximate recurrent classes from right eigenvectors.

Parameters:

• use (int | Sequence[int] | None) – Which or how many first eigenvectors to use as features for filtering and clustering. If None, use the eigengap statistic.

• percentile (int | None) – Threshold used for filtering out cells which are most likely transient states. Cells which are in the lower percentile percent of each eigenvector will be removed from the data matrix.

• method (Literal['leiden', 'kmeans']) –

  Method to be used for clustering. Valid option are:

  • 'kmeans' - KMeans.

  • 'leiden' - leiden().

• cluster_key (str | None) – Key in obs in order to associate names and colors with terminal_states.

• n_clusters_kmeans (int | None) – Number of clusters when method = 'kmeans'. If None, this is set to use + 1.

• n_neighbors (int) – Number of neighbors in a kNN graph. This is the \(K\) parameter for that, the number of neighbors for each cell. Only used when method = 'leiden'.

• resolution (float) – Resolution parameter for leiden(). Should be chosen relatively small.

• n_matches_min (int) – Filters out cells which don’t have at least n_matches_min neighbors from the same category. This filters out some cells which are transient but have been misassigned.

• n_neighbors_filtering (int) – Parameter for filtering cells. Cells are filtered out if they don’t have at least n_matches_min neighbors among the n_neighbors_filtering nearest cells.

• basis (str | None) – Key from obsm as additional features for clustering. If None, use only the right eigenvectors.

• n_comps (int) – Number of embedding components to be used when basis != None.

• scale (bool | None) – Scale the values to z-scores. If None, scale the values if basis != None.

Return type:

CFLARE

Returns:

: Returns self and just updates the following fields:

• terminal_states - Categorical annotation of terminal states.

• terminal_states_probabilities - Probability to be a terminal state.

read

static CFLARE.read(fname, adata=None, copy=False)

De-serialize self from a file.

Parameters:

• fname (str | Path) – Path from which to read the object.

• adata (AnnData | None) – AnnData object to assign to the saved object. Only used when the saved object has adata and it was saved without it.

• copy (bool) – Whether to copy adata before assigning it. If adata is a view, it is always copied.

Return type:

IOMixin

Returns:

: The de-serialized object.

rename_initial_states

CFLARE.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:

TermStatesEstimator

Returns:

: Returns self and updates the following fields:

• initial_states - Categorical annotation of initial states.

rename_terminal_states

CFLARE.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:

TermStatesEstimator

Returns:

: Returns self and updates the following fields:

• terminal_states - Categorical annotation of terminal states.

set_initial_states

CFLARE.set_initial_states(states, cluster_key=None, weight_key=None, allow_overlap=False, **kwargs)

Set the initial_states.

Parameters:

• states (Series | dict[str, Sequence[Any]]) –

  Which states to select. Valid options are:

  • categorical Series where each category corresponds to an individual state. NaN entries denote cells that do not belong to any state, i.e., transient cells.

  • dict where keys are states and values are lists of cell barcodes corresponding to annotations in obs_names. If only 1 key is provided, values should correspond to clusters if a categorical Series can be found in obs.

• cluster_key (str | Mapping[str, str] | None) – Reference annotations to associate names and colors with initial_states. Either a categorical obs column (a str or {"obs": <column>}) or {"obsm": <key>} pointing to a proportion DataFrame; see compute_macrostates().

• weight_key (str | None) – Per-observation weights, only used when cluster_key points to obsm; see compute_macrostates().

• allow_overlap (bool) – Whether to allow overlapping names between initial and terminal states.

• kwargs (Any) – Additional keyword arguments.

Return type:

TermStatesEstimator

Returns:

: Returns self and updates the following fields:

• initial_states - Categorical annotation of initial states.

• initial_states_probabilities - Probability to be an initial state.

set_terminal_states

CFLARE.set_terminal_states(states, cluster_key=None, weight_key=None, allow_overlap=False, **kwargs)

Set the terminal_states.

Parameters:

• states (Series | dict[str, Sequence[Any]]) –

  States to select. Valid options are:

  • categorical Series where each category corresponds to an individual state. NaN entries denote cells that do not belong to any state, i.e., transient cells.

  • dict where keys are states and values are lists of cell barcodes corresponding to annotations in obs_names. If only 1 key is provided, values should correspond to clusters if a categorical Series can be found in obs.

• cluster_key (str | Mapping[str, str] | None) – Reference annotations to associate names and colors with terminal_states. Either a categorical obs column (a str or {"obs": <column>}) or {"obsm": <key>} pointing to a proportion DataFrame; see compute_macrostates().

• weight_key (str | None) – Per-observation weights, only used when cluster_key points to obsm; see compute_macrostates().

• allow_overlap (bool) – Whether to allow overlapping names between initial and terminal states.

• kwargs (Any) – Additional keyword arguments.

Return type:

TermStatesEstimator

Returns:

: Returns self and updates the following fields:

• terminal_states - Categorical annotation of terminal states.

• terminal_states_probabilities - Probability to be a terminal state.

to_adata

CFLARE.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 as True or 'all', everything from this attribute will be kept.

• copy (bool | Sequence[Literal['X', 'raw', 'layers', 'obs', 'var', 'obsm', 'varm', 'obsp', 'varp', 'uns']]) – Whether to copy the data. Can be specified on per-attribute basis. Useful for attributes that are array-like.

Return type:

AnnData

Returns:

: Annotated data object.

write

CFLARE.write(fname, write_adata=True)

Serialize self to a file using pickle.

Parameters:

• fname (str | Path) – Path where to save the object.

• write_adata (bool) – Whether to save adata object.

Return type:

None

Returns:

: Nothing, just writes itself to a file.