def lineage_drivers(
adata: AnnData,
lineage: str,
backward: bool = False,
n_genes: int = 8,
ncols: Optional[int] = None,
use_raw: bool = False,
title_fmt: str = "{gene} qval={qval:.4e}",
**kwargs,
) -> None:
"""
Plot lineage drivers that were uncovered using :func:`cellrank.tl.lineage_drivers`.
Parameters
----------
%(adata)s
%(backward)s
%(plot_lineage_drivers.parameters)s
Returns
-------
%(just_plots)s
"""
pk = DummyKernel(adata, backward=backward)
mc = GPCCA(pk, read_from_adata=True, write_to_adata=False)
if use_raw and adata.raw is None:
logg.warning("No raw attribute set. Using `adata.var` instead")
use_raw = False
direction = DirPrefix.BACKWARD if backward else DirPrefix.FORWARD
needle = f"{direction} {lineage} corr"
haystack = adata.raw.var if use_raw else adata.var
if needle not in haystack:
raise RuntimeError(
f"Unable to find lineage drivers in "
f"`{'adata.raw.var' if use_raw else 'adata.var'}[{needle!r}]`. "
f"Compute lineage drivers first as `cellrank.tl.lineage_drivers(lineages={lineage!r}, "
f"use_raw={use_raw}, backward={backward}).`")
drivers = pd.DataFrame(haystack[[needle, f"{direction} {lineage} qval"]])
drivers.columns = [f"{lineage} corr", f"{lineage} qval"]
mc._set(A.LIN_DRIVERS, drivers)
mc.plot_lineage_drivers(
lineage,
n_genes=n_genes,
use_raw=use_raw,
ncols=ncols,
title_fmt=title_fmt,
**kwargs,
)
save='{}_metastable.png'.format(key))
g.plot_metastable_states(discrete=True,
show=False,
dpi=300,
legend_fontsize=0,
save='{}_discrete_metastable.pdf'.format(key),
size=28)
g.set_final_states_from_metastable_states()
if key == "H508_EV" or key == "HT29_EV":
g.compute_absorption_probabilities()
g.compute_lineage_drivers()
samples[key].var.to_csv(key + "_lineages.tsv", sep='\t')
print(samples[key].var.columns)
if key == "HT29_EV":
g.plot_lineage_drivers(
'17', save='{}_17_lineage_drivers.png'.format(key))
g.plot_lineage_drivers(
'1', save='{}_10_lineage_drivers.png'.format(key))
g.plot_lineage_drivers('11',
save='{}_1_lineage_drivers.png'.format(key))
g.plot_lineage_drivers('4',
save='{}_4_lineage_drivers.png'.format(key))
if key == "H508_EV":
g.plot_lineage_drivers(
'10', save='{}_10_lineage_drivers.png'.format(key))
g.plot_lineage_drivers(
'17', save='{}_17_lineage_drivers.png'.format(key))
g.plot_lineage_drivers('1',
save='{}_1_lineage_drivers.png'.format(key))
g.plot_lineage_drivers(