Truth#

missionbio.demultiplex.protein.truth.Truth

class Truth(celltypes: Sequence[CellType] = (), version: str = 'NA')#

A phylogenetic tree of cell types.

Parameters:

Functions#

`__init__`	param celltypes: A list of cell types.
`add_ab`	Add an antibody to a cell type and all its descendants
`add_cell`	Add a celltype to the truth.
`add_doublets`	Adds doublets to the truth.
`assert_valid`	Assert that the truth is valid.
`builtin`	The default truth for PBMCs.
`cellnames`	Returns a list of cell type names.
`complete`	returns: True, when all the celltypes contain the expression of
`copy`	Returns a deep copy of the truth.
`del_ab`	Delete an antibody from the truth.
`del_cell`	Delete a clone from the truth.
`get`	Returns the cell type with the specified name.
`has_cell`	Checks if the truth has a cell type with the specified name.
`is_panel_compatible`	Checks if the panel can be read using read_panel and is compatible with hashing.
`isolate`	Isolate the truth to only contain the given cell and its descendants.
`palette`	Get the palette of the truth.
`plot`	Plot the truth as a tree.
`read_panel`	Reads the truth from a csv panel file.
`read_yaml`	Reads a truth from a YAML file.
`set_color`	Set the color of a cell type.
`signature`	returns: A signature matrix of the truth. 1 for ab+, 0 for ab-,
`to_yaml`	Writes the truth to a YAML file.
`trim`	Trim the truth to remove the given cell and all its descendants.