def read_priors(self, priors_file=None, gold_standard_file=None):
"""
Read in the priors and gold standard files
"""
priors_file = priors_file if priors_file is not None else self.priors_file
gold_standard_file = gold_standard_file if gold_standard_file is not None else self.gold_standard_file
loader = InferelatorDataLoader(input_dir=self.input_dir, file_format_settings=self._file_format_settings)
if priors_file is not None:
Debug.vprint("Loading prior data from file {file}".format(file=priors_file), level=1)
self.priors_data = loader.input_dataframe(priors_file)
# Print debug info & check prior for duplicate indices (which will raise errors later)
self.loaded_file_info("Priors data", self.priors_data)
self._check_network_labels_unique("Priors_data", priors_file, self.priors_data)
if gold_standard_file is not None:
Debug.vprint("Loading gold_standard data from file {file}".format(file=gold_standard_file), level=1)
self.gold_standard = loader.input_dataframe(gold_standard_file)
# Print debug info & check gold standard for duplicate indices (which will raise errors later)
self.loaded_file_info("Gold standard", self.gold_standard)
self._check_network_labels_unique("Gold standard", gold_standard_file, self.gold_standard)
def load_velocity(self, velocity_file=None, loader_type=None):
velocity_file = self._velocity_file_name if velocity_file is None else velocity_file
loader_type = self._velocity_file_type if loader_type is None else loader_type
transpose = not self.expression_matrix_columns_are_genes
loader = InferelatorDataLoader(
input_dir=self.input_dir,
file_format_settings=self._file_format_settings)
Debug.vprint("Loading velocity data from {f}".format(f=velocity_file),
level=1)
if loader_type == _TSV or loader_type is None:
self._velocity_data = loader.load_data_tsv(
velocity_file, transpose_expression_data=transpose)
elif loader_type == _H5AD:
self._velocity_data = loader.load_data_h5ad(
velocity_file, use_layer=self._velocity_h5_layer)
elif loader_type == _HDF5:
self._velocity_data = loader.load_data_hdf5(
velocity_file,
transpose_expression_data=transpose,
use_layer=self._velocity_h5_layer)
else:
raise ValueError(
"Invalid velocity_file_type: {a}".format(a=loader_type))
self._velocity_data.name = "Velocity"
def validate_data(self):
"""
Make sure that the data that's loaded is acceptable
"""
# Create a null prior if the flag is set
if self.use_no_prior and self.priors_data is not None:
warnings.warn(
"The use_no_prior flag will be ignored because prior data exists"
)
elif self.use_no_prior:
Debug.vprint("A null prior is has been created", level=0)
self.priors_data = self._create_null_prior(self.data.gene_names,
self.tf_names)
# Create a null gold standard if the flag is set
if self.use_no_gold_standard and self.gold_standard is not None:
warnings.warn(
"The use_no_gold_standard flag will be ignored because gold standard data exists"
)
elif self.use_no_gold_standard:
Debug.vprint("A null gold standard has been created", level=0)
self.gold_standard = self._create_null_prior(
self.data.gene_names, self.tf_names)
# Validate that some network information exists and has been loaded
if self.priors_data is None and self.gold_standard is None:
raise ValueError("No gold standard or priors have been provided")
def make_data_noisy(data, random_seed=42):
"""
Generate a new data object of random data which matches the provided data
:param data: Raw read data
:type data: InferelatorData
:param random_seed: Random seed for data generation
:type random_seed: int
:return: Simulated data
:rtype: InferelatorData
"""
# Calculate probability vector for gene expression
# Discrete sampling for count data
sample_counts = data.sample_counts
if data._is_integer:
Debug.vprint("Simulating integer count data for {n} samples".format(
n=data.num_obs),
level=0)
# Data is centered already
if np.any(sample_counts <= 0.):
p_vec = np.ones(data.num_genes, dtype=float)
# Normalize to mean counts per sample and sum counts per gene by matrix multiplication
else:
p_vec = (np.mean(sample_counts) / sample_counts).reshape(
1, -1) @ data.expression_data
# Flatten and convert counts to a probability vector
p_vec = p_vec.flatten()
p_vec = p_vec / p_vec.sum()
data.expression_data = _sim_ints(p_vec,
sample_counts,
sparse=data.is_sparse,
random_seed=random_seed)
else:
# Data is centered already
if np.any(sample_counts <= 0.):
p_vec = np.zeros(data.num_genes, dtype=float)
# Normalize to mean total measured values per sample and sum counts per gene by matrix multiplication
else:
p_vec = (np.mean(sample_counts) / sample_counts).reshape(
1, -1) @ data.expression_data
p_vec /= data.num_obs
Debug.vprint(
"Simulating float data for {n} samples".format(n=data.num_obs),
level=0)
data.expression_data = _sim_float(p_vec.flatten(),
data.gene_stdev,
data.num_obs,
random_seed=random_seed)
def validate_data(self, check_prior=True, check_gold_standard=True):
"""
Make sure that the data that's loaded is acceptable
"""
if check_prior:
# Create a null prior if the flag is set
if self.use_no_prior and self.priors_data is not None:
warnings.warn("The use_no_prior flag will be ignored because prior data exists")
elif self.use_no_prior:
Debug.vprint("A null prior is has been created", level=0)
self.priors_data = self._create_null_prior(self._gene_names, self.tf_names)
if check_gold_standard:
# Create a null gold standard if the flag is set
if self.use_no_gold_standard and self.gold_standard is not None:
warnings.warn("The use_no_gold_standard flag will be ignored because gold standard data exists")
elif self.use_no_gold_standard:
Debug.vprint("A null gold standard has been created", level=0)
self.gold_standard = self._create_null_prior(self._gene_names, self.tf_names)
elif self.gold_standard is None:
_msg = "No gold standard found. Model scoring will be invalid. "
_msg += "Set worker.set_network_data_flags(use_no_gold_standard=True) to explicitly continue."
raise ValueError(_msg)
if check_prior and check_gold_standard:
# Validate that some network information exists and has been loaded
if self.priors_data is None and self.gold_standard is None:
raise ValueError("No gold standard or priors have been provided")
def __init__(self, X, Y):
"""
Create a regression object and do basic data transforms
:param X: Expression or Activity data [N x K]
:type X: InferelatorData
:param Y: Response expression data [N x G]
:type Y: InferelatorData
"""
# Get the IDs and total count for the genes and predictors
self.K = X.num_genes
self.tfs = X.gene_names
self.G = Y.num_genes
self.genes = Y.gene_names
# Rescale the design expression or activity data on features
self.X = X
self.X.zscore()
self.Y = Y
Debug.vprint(
"Predictor matrix {pr} and response matrix {re} ready".format(
pr=X.shape, re=Y.shape))
def run_bootstrap(self, bootstrap_idx):
betas, betas_resc = [], []
# Select the appropriate bootstrap from each task and stash the data into X and Y
for k in range(self._n_tasks):
X = self._task_design[k].get_bootstrap(self._task_bootstraps[k][bootstrap_idx])
Y = self._task_response[k].get_bootstrap(self._task_bootstraps[k][bootstrap_idx])
# Make sure that the priors align to the expression matrix
priors_data = self._task_priors[k].reindex(labels=self._targets, axis=0). \
reindex(labels=self._regulators, axis=1). \
fillna(value=0)
if self.clr_only:
# Create a mock prior with no information if clr_only is set
priors_data = pd.DataFrame(0, index=priors_data.index, columns=priors_data.columns)
MPControl.sync_processes(pref="bbsr_pre")
Debug.vprint('Calculating MI, Background MI, and CLR Matrix', level=0)
clr_matrix, _ = self.mi_driver().run(Y, X, return_mi=False)
Debug.vprint('Calculating task {k} betas using BBSR'.format(k=k), level=0)
t_beta, t_br = BBSR(X, Y, clr_matrix, priors_data,
prior_weight=self.prior_weight, no_prior_weight=self.no_prior_weight,
nS=self.bsr_feature_num).run()
betas.append(t_beta)
betas_resc.append(t_br)
return betas, betas_resc
def compute_common_data(self):
"""
Compute common data structures like design and response matrices.
"""
drd = self.drd_driver(
metadata_handler=self.metadata_handler,
return_half_tau=True) if self.drd_driver is not None else None
# If there is no design-response driver set, use the expression data for design and response
# Also do this if there is no usable metadata
if drd is None or not drd.validate_run(self.data.meta_data):
self.design, self.response, self.half_tau_response = self.data, self.data, self.data
# Otherwise calculate the design-response ODE
# TODO: Rewrite DRD for InferelatorData
# TODO: This is *horrifying* as is from a memory perspective
# TODO: Really fix this soon
else:
Debug.vprint('Creating design and response matrix ... ')
drd.delTmin, drd.delTmax, drd.tau = self.delTmin, self.delTmax, self.tau
design, response, half_tau_response = drd.run(
self.data.to_df().T, self.data.meta_data)
self.design = InferelatorData(design.T)
self.response = InferelatorData(response.T)
self.half_tau_response = InferelatorData(half_tau_response.T)
Debug.vprint("Constructed design {d} and response {r} matrices".format(
d=self.design.shape, r=self.response.shape),
level=1)
self.data = None
def load_activity(self, file=None, file_type=None):
file = self._tfa_input_file if file is None else file
file_type = self._tfa_input_file_type if file_type is None else file_type
loader = InferelatorDataLoader(
input_dir=self.input_dir,
file_format_settings=self._file_format_settings)
if file_type.lower() == "h5ad":
self.design = loader.load_data_h5ad(file)
elif self._expression_loader.lower() == "tsv":
self.design = loader.load_data_tsv(file)
Debug.vprint("Loaded {f} as design matrix {d}".format(
d=self.design.shape, f=file),
level=1)
self.design.trim_genes(
remove_constant_genes=False,
trim_gene_list=self.design.gene_names.intersection(self.tf_names))
Debug.vprint("Trimmed to {d} for TF activity".format(
d=self.design.shape, f=file),
level=1)
assert check.indexes_align(
[self.design.sample_names, self.response.sample_names])
def filter_to_gene_list(self):
"""
Filter the priors and expression matrix to just genes in gene_metadata
"""
Debug.vprint("Trimming expression matrix", level=1)
self.data.trim_genes(trim_gene_list=self.gene_names)
self.priors_data = self.prior_manager.filter_priors_to_genes(self.priors_data, self.data.gene_names)
def _check_file_exists(self, file_name):
"""
Print a warning if a file doesn't exist
:param file_name: str
"""
if file_name is not None and not os.path.isfile(self.input_path(file_name)):
Debug.vprint("File {f} does not exist".format(f=file_name), level=0)
def trim_genes(self, remove_constant_genes=True, trim_gene_list=None):
"""
Remove genes (columns) that are unwanted from the data set. Do this in-place.
:param remove_constant_genes:
:type remove_constant_genes: bool
:param trim_gene_list: This is a list of genes to KEEP.
:type trim_gene_list: list, pd.Series, pd.Index
"""
keep_column_bool = np.ones((len(self._adata.var_names),), dtype=bool)
if trim_gene_list is not None:
keep_column_bool &= self._adata.var_names.isin(trim_gene_list)
if "trim_gene_list" in self._adata.uns:
keep_column_bool &= self._adata.var_names.isin(self._adata.uns["trim_gene_list"])
list_trim = len(self._adata.var_names) - np.sum(keep_column_bool)
comp = 0 if self._is_integer else np.finfo(self.values.dtype).eps * 10
if remove_constant_genes:
nz_var = self.values.max(axis=0) - self.values.min(axis=0)
nz_var = nz_var.A.flatten() if self.is_sparse else nz_var
if np.any(np.isnan(nz_var)):
raise ValueError("NaN values are present in the expression matrix; unable to remove var=0 genes")
nz_var = comp < nz_var
keep_column_bool &= nz_var
var_zero_trim = np.sum(nz_var)
else:
var_zero_trim = 0
if np.sum(keep_column_bool) == 0:
err_msg = "No genes remain after trimming. ({lst} removed to match list, {v} removed for var=0)"
raise ValueError(err_msg.format(lst=list_trim, v=var_zero_trim))
if np.sum(keep_column_bool) == self._adata.shape[1]:
pass
else:
Debug.vprint("Trimming {name} matrix {sh} to {n} columns".format(name=self.name, sh=self._adata.X.shape,
n=np.sum(keep_column_bool)),
level=1)
# This explicit copy allows the original to be deallocated
# Otherwise the GC leaves the original because the view reference keeps it alive
# At some point it will need to copy so why not now
self._adata = AnnData(self._adata.X[:, keep_column_bool],
obs=self._adata.obs.copy(),
var=self._adata.var.loc[keep_column_bool, :].copy(),
dtype=self._adata.X.dtype)
# Make sure that there's no hanging reference to the original object
gc.collect()
def _recalculate_design(self):
"""
Use the TFA driver to recalculate the design matrix
"""
self.design.convert_to_float()
self.half_tau_response.convert_to_float()
self.design = self.tfa_driver().compute_transcription_factor_activity(
self.priors_data, self.design, self.half_tau_response)
Debug.vprint("Rebuilt design matrix {d} with TF activity".format(
d=self.design.shape),
level=1)
def set_expression_file(self, tsv=None, hdf5=None, h5ad=None, tenx_path=None, mtx=None, mtx_barcode=None,
mtx_feature=None, h5_layer=None):
"""
Set the type of expression data file. Current loaders include TSV, hdf5, h5ad (AnnData), and MTX sparse files.
Only one of these loaders can be used; passing arguments for multiple loaders will raise a ValueError.
:param tsv: A path to a TSV (or tsv.gz) file which can be loaded by pandas.read_csv()
:type tsv: str, optional
:param hdf5: A path to a hdf5 file which can be loaded by pandas.HDFStore
:type hdf5: str, optional
:param h5ad: A path to an AnnData hd5 file
:type h5ad: str, optional
:param tenx_path: A path to the folder containing the 10x mtx, barcode, and feature files
:type tenx_path: Path, optional
:param mtx: A path to an mtx file
:type mtx: str, optional
:param mtx_barcode: A path to a list of observation names (i.e. barcodes, etc) for the mtx file
:type mtx_barcode: str, optional
:param mtx_feature: A path to a list of gene names for the mtx file
:type mtx_feature: str, optional
:param h5_layer: The layer (in an AnnData h5) or the store key (in an hdf5) file to use.
Defaults to using the first key.
:type h5_layer: str, optional
"""
nones = [tsv is None, hdf5 is None, h5ad is None, tenx_path is None, mtx is None]
if all(nones):
Debug.vprint("No file provided", level=0)
elif sum(nones) != (len(nones) - 1):
raise ValueError("Only one type of input expression file can be set")
if tsv is not None:
self._set_file_name("expression_matrix_file", tsv)
self._expression_loader = _TSV
elif hdf5 is not None:
self._set_file_name("expression_matrix_file", hdf5)
self._expression_loader = _HDF5
self._h5_layer = h5_layer
elif h5ad is not None:
self._set_file_name("expression_matrix_file", h5ad)
self._expression_loader = _H5AD
self._h5_layer = h5_layer
elif mtx is not None:
self._check_file_exists(mtx)
self._check_file_exists(mtx_barcode)
self._check_file_exists(mtx_feature)
self.expression_matrix_file = (mtx, mtx_barcode, mtx_feature)
self._expression_loader = _MTX
elif tenx_path is not None:
self.expression_matrix_file = tenx_path
self._expression_loader = _TENX
def filter_to_gene_list(self):
"""
Filter the priors and expression matrix to just genes in gene_metadata
"""
# Most operations will be column-wise; change sparse type if needed here
Debug.vprint("Preparing to trim expression matrix", level=2)
self.data.to_csc()
Debug.vprint("Trimming expression matrix", level=1)
self.data.trim_genes(trim_gene_list=self.gene_names)
self.priors_data = self.prior_manager.filter_priors_to_genes(
self.priors_data, self.data.gene_names)
def _get_file_name_from_attribute(self, file_name):
"""
Check and see if a file name is an object attribute that holds a file namee
:param file_name: str
:return file_name: str
"""
# Check and see if file_name is actually an object attribute holding a file name. Use that if so.
if file_name not in self._file_format_settings:
if hasattr(self, file_name) and getattr(self, file_name) in self._file_format_settings:
file_name = getattr(self, file_name)
else:
Debug.vprint("File {f} is unknown".format(f=file_name), level=0)
return None
return file_name
def get_data(self):
"""
Load all the data and then return a list of references to TaskData objects
There will be multiple objects returned if tasks_from_metadata is set.
If tasks_from_metadata is not set, the list contains only this task (self)
:return: List of TaskData objects with loaded data
:rtype: list(TaskData)
"""
Debug.vprint("Loading data for task {task_name}".format(task_name=self.task_name))
super(TaskData, self).get_data()
if self.tasks_from_metadata:
return self.separate_tasks_by_metadata()
else:
return [self]
def print_file_loading_arguments(self, file_name):
"""
Print the settings that will be used to load a given file name.
:param file_name: The name of the variable containing the file name (from `set_file_properties`)
:type file_name: str
"""
# Check and see if file_name is actually an object attribute holding a file name. Use that if so.
file_name = self._get_file_name_from_attribute(file_name)
if file_name is None:
return
msg = "File {f} has the following settings:".format(f=file_name)
msg += "\n\t".join([str(k) + " = " + str(v) for k, v in self._file_format_settings[file_name].items()])
Debug.vprint(msg, level=0)
def run_regression(self):
betas = []
rescaled_betas = []
for idx, bootstrap in enumerate(self.get_bootstraps()):
Debug.vprint('Bootstrap {} of {}'.format((idx + 1),
self.num_bootstraps),
level=0)
np.random.seed(self.random_seed + idx)
current_betas, current_rescaled_betas = self.run_bootstrap(
bootstrap)
betas.append(current_betas)
rescaled_betas.append(current_rescaled_betas)
return betas, rescaled_betas
def run_regression(self):
betas = [[] for _ in range(self._n_tasks)]
rescaled_betas = [[] for _ in range(self._n_tasks)]
for idx in range(self.num_bootstraps):
Debug.vprint('Bootstrap {} of {}'.format((idx + 1),
self.num_bootstraps),
level=0)
current_betas, current_rescaled_betas = self.run_bootstrap(idx)
for k in range(self._n_tasks):
betas[k].append(current_betas[k])
rescaled_betas[k].append(current_rescaled_betas[k])
return betas, rescaled_betas
def _check_network_labels_unique(df_name, file_name, df, raise_on_duplicate=False):
_msg = None
if not df.columns.is_unique:
_repeated = df.columns[df.columns.duplicated()]
_msg = "{name} {f}: {n} TFs are duplicated ({g})"
Debug.vprint(_msg.format(name=df_name, f=file_name, n=len(_repeated), g=" ".join(_repeated)), level=0)
if not df.index.is_unique:
_repeated = df.index[df.index.duplicated()]
_msg = "{name} {f}: {n} Genes are duplicated ({g})"
Debug.vprint(_msg.format(name=df_name, f=file_name, n=len(_repeated), g=" ".join(_repeated)), level=0)
if _msg is not None and raise_on_duplicate:
raise ValueError(_msg)
def separate_tasks_by_metadata(self, meta_data_column=None):
"""
Take a single expression matrix and break it into multiple dataframes based on meta_data. Return a list of
TaskData objects which have the task-specific data loaded into them
:param meta_data_column: Meta_data column which corresponds to task ID
:type meta_data_column: str
:return new_task_objects: List of the TaskData objects with only one task's data each
:rtype: list(TaskData)
"""
if self.data is None:
raise ValueError("No data has been loaded prior to `separate_tasks_by_metadata`")
meta_data_column = meta_data_column if meta_data_column is not None else self.meta_data_task_column
if meta_data_column is None:
raise ValueError("tasks_from_metadata is set but meta_data_task_column is not")
elif meta_data_column not in self.data.meta_data:
msg = "meta_data_task_column is not found in task {t}".format(t=str(self))
raise ValueError(msg)
new_task_objects = list()
tasks = self.data.meta_data[meta_data_column].unique().tolist()
Debug.vprint("Creating {n} tasks from metadata column {col}".format(n=len(tasks), col=meta_data_column),
level=0)
# Remove data references from self
data = self.data
self.data = None
for task in tasks:
# Copy this object
task_obj = copy.deepcopy(self)
# Get an index of the stuff to keep
task_idx = data.meta_data[meta_data_column] == task
# Reset expression matrix, metadata, and task_name in the copy
task_obj.data = data.subset_copy(row_index=task_idx)
task_obj.data.name = task
task_obj.task_name = task
new_task_objects.append(task_obj)
Debug.vprint("Separated data into {ntask} tasks".format(ntask=len(new_task_objects)), level=0)
return new_task_objects
def read_tfs(self, file=None):
"""
Read tf names file into tf_names
"""
# Load the class variable if no file is passed
file = self.tf_names_file if file is None else file
if file is not None:
Debug.vprint("Loading TF feature names from file {file}".format(file=file), level=1)
# Read in a dataframe with no header or index
loader = InferelatorDataLoader(input_dir=self.input_dir, file_format_settings=self._file_format_settings)
tfs = loader.input_dataframe(file, header=None, index_col=None)
# Cast the dataframe into a list
assert tfs.shape[1] == 1
self.tf_names = tfs.values.flatten().tolist()
def _align_velocity(self):
keep_genes = self._velocity_data.gene_names.intersection(
self.data.gene_names)
Debug.vprint(
"Aligning velocity and expression data on {n} genes".format(
n=len(keep_genes)))
self._velocity_data.trim_genes(remove_constant_genes=False,
trim_gene_list=keep_genes)
self.data.trim_genes(remove_constant_genes=False,
trim_gene_list=keep_genes)
assert check.indexes_align(
(self._velocity_data.gene_names, self.data.gene_names))
assert check.indexes_align(
(self._velocity_data.sample_names, self.data.sample_names))
def pileup_data(self, run_data):
"""
Take the completed run data and pack it up into a DataFrame of betas
:param run_data: list
A list of regression result dicts ordered by gene. Each regression result should have `ind`, `pp`, `betas`
and `betas_resc` keys with the appropriate data.
:return betas, betas_rescale: (pd.DataFrame [G x K], pd.DataFrame [G x K])
"""
# Create G x K arrays of 0s to populate with the regression data
betas = np.zeros((self.G, self.K), dtype=np.dtype(float))
betas_rescale = np.zeros((self.G, self.K), dtype=np.dtype(float))
# Populate the zero arrays with the BBSR betas
for data in run_data:
# If data is None assume a null model
if data is None:
raise RuntimeError("No model produced by regression method")
xidx = data['ind'] # Int
yidx = data['pp'] # Boolean array of size K
betas[xidx, yidx] = data['betas']
betas_rescale[xidx, yidx] = data['betas_resc']
d_len, b_avg, null_m = self._summary_stats(betas)
Debug.vprint("Regression complete:", end=" ", level=0)
Debug.vprint(
"{d_len} Models, {b_avg} Preds per Model ({nom} Null)".format(
d_len=d_len, b_avg=round(b_avg, 4), nom=null_m),
level=0)
# Convert arrays into pd.DataFrames to return results
betas = pd.DataFrame(betas,
index=self.Y.gene_names,
columns=self.X.gene_names)
betas_rescale = pd.DataFrame(betas_rescale,
index=self.Y.gene_names,
columns=self.X.gene_names)
return betas, betas_rescale
def run_regression(self):
betas = []
rescaled_betas = []
MPControl.sync_processes("pre_regression")
for idx, bootstrap in enumerate(self.get_bootstraps()):
Debug.vprint('Bootstrap {} of {}'.format((idx + 1),
self.num_bootstraps),
level=0)
np.random.seed(self.random_seed + idx)
current_betas, current_rescaled_betas = self.run_bootstrap(
bootstrap)
if self.is_master():
betas.append(current_betas)
rescaled_betas.append(current_rescaled_betas)
MPControl.sync_processes("post_bootstrap")
return betas, rescaled_betas
def read_genes(self, file=None):
"""
Read gene names file into gene_names
"""
# Load the class variable if no file is passed
file = self.gene_names_file if file is None else file
if file is not None:
Debug.vprint("Loading Gene feature names from file {file}".format(file=file), level=1)
# Read in a dataframe with no header or index
loader = InferelatorDataLoader(input_dir=self.input_dir, file_format_settings=self._file_format_settings)
genes = loader.input_dataframe(file, header=None, index_col=None)
# Cast the dataframe into a list
assert genes.shape[1] == 1
self.gene_names = genes.values.flatten().tolist()
# Use the gene names in the data file if no restrictive list is provided
if self.gene_names is None and self.data is not None:
self.gene_names = self.data.gene_names.copy()
def set_mkl(cls, mkl=True):
# If the MKL flag is None, don't change anything
if mkl is None:
pass
# If the MKL flag is True, use the dot_product_mkl function when .dot() is called
if mkl:
try:
from sparse_dot_mkl import get_version_string, dot_product_mkl as dp
msg = "Matrix multiplication will use sparse_dot_mkl package with MKL: {m}"
vstring = get_version_string()
Debug.vprint(msg.format(m=vstring if vstring is not None else "Install mkl-service for details"),
level=2)
cls._dot_func = dp
# If it isn't available, use the scipy/numpy functions instead
except ImportError as err:
Debug.vprint("Unable to load MKL with sparse_dot_mkl:\n" + str(err), level=0)
cls._dot_func = dot_product
# If the MKL flag is True, use the python (numpy/scipy) functions when .dot() is called
else:
Debug.vprint("Matrix multiplication will use Numpy; this is not advised for sparse data", level=2)
cls._dot_func = dot_product
def _combine_expression_velocity(self, expression, velocity):
"""
Calculate dX/dt + lambda * X
:param expression:
:param velocity:
:return:
"""
assert check.indexes_align(
(expression.gene_names, velocity.gene_names))
assert check.indexes_align(
(expression.sample_names, velocity.sample_names))
if self._decay_constants is not None:
Debug.vprint("Using preloaded decay constants in _decay_constants")
decay_constants = self._decay_constants
elif self.tau is not None:
Debug.vprint(
"Calculating decay constants for tau {t}".format(t=self.tau))
decay_constants = np.repeat(1 / self.tau, expression.num_genes)
elif "decay_constants" in velocity.gene_data.columns and self._use_precalculated_decay_constants:
Debug.vprint(
"Extracting decay constants from {n}".format(n=velocity.name))
decay_constants = velocity.gene_data["decay_constants"].values
elif "decay_constants" in expression.gene_data.columns and self._use_precalculated_decay_constants:
Debug.vprint("Extracting decay constants from {n}".format(
n=expression.name))
decay_constants = expression.gene_data["decay_constants"].values
else:
Debug.vprint(
"No decay information found. Solving dX/dt = AB for Betas")
return velocity
x = np.multiply(expression.values, decay_constants[None, :])
return InferelatorData(np.add(velocity.values, x),
gene_names=expression.gene_names,
sample_names=expression.sample_names,
meta_data=expression.meta_data)
def read_priors(self, priors_file=None, gold_standard_file=None):
"""
Read in the priors and gold standard files
"""
priors_file = priors_file if priors_file is not None else self.priors_file
gold_standard_file = gold_standard_file if gold_standard_file is not None else self.gold_standard_file
loader = InferelatorDataLoader(
input_dir=self.input_dir,
file_format_settings=self._file_format_settings)
if priors_file is not None:
Debug.vprint(
"Loading prior data from file {file}".format(file=priors_file),
level=1)
self.priors_data = loader.input_dataframe(priors_file)
self.loaded_file_info("Priors data", self.priors_data)
if gold_standard_file is not None:
Debug.vprint("Loading gold_standard data from file {file}".format(
file=gold_standard_file),
level=1)
self.gold_standard = loader.input_dataframe(gold_standard_file)
self.loaded_file_info("Gold standard", self.gold_standard)
