glue_genes.glue_single_cell.data.DataAnnData#

class glue_genes.glue_single_cell.data.DataAnnData(label='', full_anndata_obj=None, backed=False, coords=None, **kwargs)#

A Data class to handle on-disk and sparse access to a large AnnData X matrix.

Attributes:

Xdata: The full AnnData object, accessible for analysis functions that need one.
listenerslist: Any GeneSummaryListener associated with this object.
backedbool: True if the matrix is not loaded into memory but is accessed from the disk.
sparsebool: True if the underlying matrix is sparse

__init__(label='', full_anndata_obj=None, backed=False, coords=None, **kwargs)#

Methods

`__init__`([label, full_anndata_obj, backed, ...])
`add_component`(component, label)	Add a new component to this data set.
`add_component_link`(link[, label])	Shortcut method for generating a new `DerivedComponent` from a ComponentLink object, and adding it to a data set.
`add_subset`(subset[, label])	Assign a pre-existing subset to this data object.
`broadcast`(attribute)	Send a `DataUpdateMessage` to the hub
`component_ids`()	Equivalent to `Data.components`
`compute_fixed_resolution_buffer`(args, *kwargs)	Get a fixed-resolution buffer.
`compute_histogram`(cids[, weights, range, ...])	Compute an n-dimensional histogram with regularly spaced bins.
`compute_statistic`(statistic, cid[, axis, ...])	Compute a statistic for the data.
`dtype`(cid)	Lookup the dtype for the data associated with a ComponentID
`find_component_id`(label)	Retrieve component_ids associated by label name.
`get_component`(component_id)	Fetch the component corresponding to component_id.
`get_data`(cid[, view, keep_sparse])	Get the data values for a given component.
`get_kind`(cid)	Get the kind of data for a given component.
`get_mask`(subset_state[, view])	Do not allow subset_states to propagate through X matrix.
`get_object`([cls])	Get the dataset represented as a non-glue object, using the translation infrastructure.
`get_selection_definition`([subset_id, format])	Get subset state represented as a non-glue object, using the translation infrastructure.
`get_subset_object`([subset_id, cls])	Get a subset represented as a non-glue object, using the translation infrastructure.
`join_on_key`(other, cid, cid_other)	Create an element mapping to another dataset, by joining on values of ComponentIDs in both datasets.
`new_subset`([subset])	Create a new subset, and attach to self.
`register_to_hub`(hub)	Connect to a hub.
`remove_component`(component_id)	Remove a component from a data set
`reorder_components`(component_ids)	Reorder the components using a list of component IDs.
`to_dataframe`([index])	Convert the Data object into a `pandas.DataFrame` object.
`update_components`(mapping)	Change the numerical data associated with some of the Components in this Data object.
`update_id`(old, new)	Reassign a component to a different `glue.core.component_id.ComponentID`
`update_values_from_data`(data)	Replace numerical values in data to match values from another dataset.

Attributes

`Xdata`	The full AnnData object, accessible for analysis functions that need one.
`components`	All `ComponentIDs` in the Data.
`coordinate_components`	The ComponentIDs associated with a `CoordinateComponent`.
`coordinate_links`	A list of the ComponentLinks that connect pixel and world.
`coords`	The coordinates object for the data.
`data`
`derived_components`	The ComponentIDs for each `DerivedComponent`.
`derived_links`	A list of the links present inside all of the DerivedComponent objects in this dataset.
`externally_derivable_components`
`label`	The name of the dataset
`links`	A list of all the links internal to the dataset.
`main_components`
`ndim`	The number of dimensions of the data, as an integer.
`pixel_aligned_data`	Information about other datasets in the same data collection that have matching or a subset of pixel component IDs.
`pixel_component_ids`	The `ComponentIDs` for each pixel coordinate.
`primary_components`	The ComponentIDs not associated with a `DerivedComponent`
`shape`	The n-dimensional shape of the dataset, as a tuple.
`size`	The size of the data (the product of the shape dimensions), as an integer.
`subsets`	Tuple of subsets attached to this dataset.
`visible_components`	All `ComponentIDs` in the Data that aren't coordinates.
`world_component_ids`	The `ComponentIDs` for each world coordinate.