Package index • dafr

Core DAF Functionality

Core functions for working with Daf objects

Daf(): Daf (Data Axes Format) S3 object
is_daf(): Check if object is a Daf
print(<Daf>): Print method for Daf objects
description(): Get description of a Daf object
`[`(<Daf>): Extract results from a Daf object using a query
setup_daf(): Set up of the Julia environment needed for DataAxesFormats and TanayLabUtilities
use_default_julia_environment(): Use default or custom Julia environment
install_daf_packages(): Install Julia packages needed for DataAxesFormats and TanayLabUtilities
load_daf_packages(): Load Julia packages needed for DataAxesFormats and TanayLabUtilities
daf_name() name(): Gets the name of a Daf object

AnnData Facade

AnnData-like live facade for Daf objects

DafAnnData: AnnData-like live facade for a Daf object
as_anndata(): Create an AnnData-like facade for a Daf object

Example Data

Functions for loading example data

example_cells_daf(): Load example cells data into a Daf object
example_metacells_daf(): Load example metacells data into a Daf object
example_chain_daf(): Load example chain data into a Daf object

Data Access and Query

Functions for querying and retrieving data from Daf objects

get_dataframe() get_tidy(): Get a dataframe from a Daf object
get_dataframe_query(): Apply a query to a Daf object and return result as a data.frame
get_empty_dense_matrix(): Get an empty dense matrix for filling
get_empty_dense_vector(): Get an empty dense vector for filling
get_empty_sparse_matrix(): Get an empty sparse matrix for filling
get_empty_sparse_vector(): Get an empty sparse vector for filling
get_frame(): Get a dataframe from a Daf object (Julia-style)
get_matrix(): Get matrix from a Daf object
get_query(): Apply a query to a Daf object
get_scalar(): Get scalar value from a Daf object
get_vector(): Get vector from a Daf object
has_query(): Check if a query can be applied to a Daf object
parse_query(): Parse a query string into a query object
query_result_dimensions(): Get the number of dimensions of a query result
is_axis_query(): Check if a query returns axis entries
query_axis_name(): Get the axis name from a query
query_requires_relayout(): Check if a query requires relayout
escape_value(): Escape a value for use in a query string
unescape_value(): Unescape a value from a query string

Readers and Formats

Reading Daf data from different sources and formats

memory_daf(): Create a Daf object with in-memory storage
h5df(): Create a Daf object with HDF5-based storage
files_daf(): Create a Daf object with file-based storage
h5ad_as_daf(): Convert h5ad file to a Daf object
read_only(): Create a read-only wrapper for a Daf object
chain_reader(): Create a read-only chain wrapper of DafReader objects
complete_daf(): Complete chain of Daf repositories
complete_chain(): Create a persistent chain from a base Daf and a new Daf
complete_path(): Get the complete filesystem path of a persistent Daf repository
open_daf(): Open a Daf repository based on path

Writers

Writing Daf data to different formats

daf_as_h5ad(): Convert Daf object to h5ad file
chain_writer(): Create a writable chain wrapper of DafReader objects

Constants and Handlers

Constants and handler functions

ALL_AXES: All axes specifier
ALL_MATRICES: All matrices specifier
ALL_SCALARS: All scalars specifier
ALL_VECTORS: All vectors specifier
VIEW_ALL_AXES: View all axes specifier
VIEW_ALL_DATA: View all data specifier
VIEW_ALL_MATRICES: View all matrices specifier
VIEW_ALL_SCALARS: View all scalars specifier
VIEW_ALL_VECTORS: View all vectors specifier
IGNORE_HANDLER WARN_HANDLER ERROR_HANDLER: Handler types for abnormal operations
inefficient_action_handler(): Set the handler for inefficient matrix access

Axes and Properties

Functions for managing axes and properties in Daf objects

has_axis(): Check if an axis exists in a Daf object
add_axis(): Add axis to a Daf object
delete_axis(): Delete axis from a Daf object
axis_contract(): Create an axis contract specification
axis_dict(): Get dictionary of axis entries to indices
axis_entries(): Get entry names for indices in an axis
axis_indices(): Get indices of entries in an axis
axis_length(): Get length of an axis in a Daf object
axis_vector(): Get vector of axis entries from a Daf object
axis_version_counter(): Get axis version counter
axes_set(): Get set of axis names from a Daf object
matrices_set(): Get set of matrix names for axes in a Daf object
scalars_set(): Get set of scalar names from a Daf object
vectors_set(): Get set of vector names for an axis in a Daf object
has_scalar(): Check if a scalar exists in a Daf object
has_vector(): Check if a vector exists in a Daf object
has_matrix(): Check if a matrix exists in a Daf object
delete_matrix(): Delete matrix from a Daf object
delete_scalar(): Delete scalar from a Daf object
delete_vector(): Delete vector from a Daf object
get_matrix(): Get matrix from a Daf object
get_scalar(): Get scalar value from a Daf object
get_vector(): Get vector from a Daf object
set_matrix(): Set matrix in a Daf object
set_scalar(): Set scalar value in a Daf object
set_vector(): Set vector in a Daf object
relayout_matrix(): Relayout matrix in a Daf object
matrix_version_counter(): Get matrix version counter
vector_version_counter(): Get vector version counter
get_empty_dense_vector(): Get an empty dense vector for filling
get_empty_sparse_vector(): Get an empty sparse vector for filling
get_empty_dense_matrix(): Get an empty dense matrix for filling
get_empty_sparse_matrix(): Get an empty sparse matrix for filling
filled_empty_sparse_vector(): Signal that an empty sparse vector has been filled
filled_empty_sparse_matrix(): Signal that an empty sparse matrix has been filled

Query Operations - Element-wise

Element-wise operations that preserve data shape but transform values

Abs(): Abs query operation
Clamp(): Clamp query operation
Convert(): Convert query operation
Fraction(): Fraction query operation
Log(): Log query operation
Round(): Round query operation
Significant(): Significant query operation

Query Operations - Reduction

Reduction operations that reduce dimensions (matrix to vector, vector to scalar)

Sum(): Sum query operation
Mean(): Mean query operation
Median(): Median query operation
Min(): Min query operation
Max(): Max query operation
Var(): Var query operation
VarN(): VarN query operation
Std(): Std query operation
StdN(): StdN query operation
Quantile(): Quantile query operation
Count(): Count query operation
GeoMean(): GeoMean query operation
Mode(): Mode query operation
CountBy(): CountBy query operation
GroupBy(): GroupBy query operation
GroupColumnsBy(): GroupColumnsBy query operation
GroupRowsBy(): GroupRowsBy query operation
ReduceToColumn(): ReduceToColumn query operation
ReduceToRow(): ReduceToRow query operation

Query Operations - Logical

Logical operations for filtering and combining data

And() AndMask(): AndMask query operation
AndNot() AndNegatedMask(): AndNegatedMask query operation
Or() OrMask(): OrMask query operation
OrNot() OrNegatedMask(): OrNegatedMask query operation
Xor() XorMask(): XorMask query operation
XorNot() XorNegatedMask(): XorNegatedMask query operation
IsEqual(): IsEqual query operation
IsGreater(): IsGreater query operation
IsGreaterEqual(): IsGreaterEqual query operation
IsLess(): IsLess query operation
IsLessEqual(): IsLessEqual query operation
IsMatch(): IsMatch query operation
IsNotEqual(): IsNotEqual query operation
IsNotMatch(): IsNotMatch query operation

Query Operations - Selection

Operations for selecting data from axes and properties

Axis(): Axis query operation
Lookup() LookupVector(): LookupVector query operation
LookupScalar(): LookupScalar query operation
LookupMatrix(): LookupMatrix query operation
Names(): Names query operation
AsAxis(): AsAxis query operation
Fetch(): Fetch (Deprecated)
IfMissing(): IfMissing query operation
IfNot(): IfNot query operation
BeginMask(): BeginMask query operation
BeginNegatedMask(): BeginNegatedMask query operation
EndMask(): EndMask query operation
MaskSlice(): MaskSlice (Deprecated)
SquareMaskColumn() SquareColumnIs(): SquareColumnIs query operation
SquareMaskRow() SquareRowIs(): SquareRowIs query operation

Views and Adapters

Creating views and adapters for Daf objects

adapter(): Invoke a computation on a view of some data set and return the result
viewer(): Create a read-only view of a Daf data set
reconstruct_axis(): Reconstruct implicit axes

Contracts

Contract-based validation for Daf objects

RequiredInput OptionalInput GuaranteedOutput OptionalOutput: Contract Expectation Types
create_contract(): Create a Contract specification
contractor(): Create a contract-aware wrapper for a Daf
contract_docs(): Convert contract to documentation string
verify_contract(): Verify a DAF object against a contract
verify_input(): Verify DAF input against contract
verify_output(): Verify DAF output against contract
print(<DafContract>): Print method for DafContract
scalar_contract(): Create a scalar contract specification
vector_contract(): Create a vector contract specification
matrix_contract(): Create a matrix contract specification
tensor_contract(): Create a tensor contract specification

Groups

Functions for working with groups of axis entries

group_names(): Generate names for groups of axis entries
compact_groups(): Compact group indices
collect_group_members(): Collect group members from group indices

Data Operations

Operations for transforming and combining Daf objects

concatenate(): Concatenate multiple Daf data sets along some axis
copy_all(): Copy all content from source to destination
copy_axis(): Copy an axis from source to destination
copy_matrix(): Copy a matrix from source to destination
copy_scalar(): Copy a scalar from source to destination
copy_tensor(): Copy a tensor from source to destination
copy_vector(): Copy a vector from source to destination

Utilities

Utility functions for working with Daf objects

empty_cache(): Empty cache of a Daf object
set_seed(): Set a seed both in Julia and R
setup_logger(): Set up a global logger

Deprecated

Deprecated functions and their replacements

deprecated-queries: Deprecated query operations
And() AndMask(): AndMask query operation
AndNot() AndNegatedMask(): AndNegatedMask query operation
Or() OrMask(): OrMask query operation
OrNot() OrNegatedMask(): OrNegatedMask query operation
Xor() XorMask(): XorMask query operation
XorNot() XorNegatedMask(): XorNegatedMask query operation