Truth

missionbio.demultiplex.protein.truth.Truth

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

A phylogenetic tree of cell types.

Input and Output

copy()	Returns a deep copy of the truth.
read_panel(path)	Reads the truth from a csv panel file.
read_yaml(path)	Reads a truth from a YAML file.
to_yaml(path, version)	Writes the truth to a YAML file.
signature()	returns: A signature matrix of the truth. 1 for ab+, 0 for ab-,

Handling

cellnames()	Returns a list of cell type names.
add_doublets()	Adds doublets to the truth.
get()	Returns the cell type with the specified name.
has_cell(cell)	Checks if the truth has a cell type with the specified name.
add_cell(cell, expression[, parent, append, ...])	Add a celltype to the truth.
del_cell(name[, check_valid])	Delete a clone from the truth.
add_ab(expression, cell)	Add an antibody to a cell type and all its descendants
del_ab(antibody[, cell])	Delete an antibody from the truth.
trim(name[, include, check_valid])	Trim the truth to remove the given cell and all its descendants.
isolate(name[, include, check_valid])	Isolate the truth to only contain the given cell and its descendants.

Plotting

set_color(name, color[, recursive])	Set the color of a cell type.
palette()	Get the palette of the truth.
plot([cutoff, width, unique])	Plot the truth as a tree.

Validity checks

complete()	returns: True, when all the celltypes contain the expression of
is_panel_compatible(path)	Checks if the panel can be read using read_panel and is compatible with hashing.
assert_valid()	Assert that the truth is valid.

param celltypes:

A list of cell types.

param version:

The version of the truth.