cellrank.pl.aggregate_fate_probabilities¶
- cellrank.pl.aggregate_fate_probabilities(adata, mode='paga_pie', backward=False, lineages=None, cluster_key='clusters', clusters=None, basis=None, cbar=True, ncols=None, sharey=False, fmt='0.2f', xrot=90, legend_kwargs=mappingproxy({'loc': 'best'}), figsize=None, dpi=None, save=None, **kwargs)[source]¶
Plot aggregate lineage probabilities at a cluster level.
This can be used to investigate how likely a certain cluster is to go to the terminal states, or in turn to have descended from the initial states. For mode ‘paga’ and ‘paga_pie’, we use PAGA [Wolf et al., 2019].
- Parameters:
adata (
AnnData
) – Annotated data object.mode (
Literal
['bar'
,'paga'
,'paga_pie'
,'violin'
,'heatmap'
,'clustermap'
]) –Type of plot to show. Valid options are:
'bar'
- barplot, one panel per cluster. The whiskers correspond to the standard error of the mean.'paga'
-paga()
, one per initial or terminal state, colored in by fate.'paga_pie'
-paga()
with pie charts indicating aggregated fates.'violin'
- violin plots, one per initial or terminal state.'heatmap'
- a heatmap, showing average fates per cluster.'clustermap'
- same as a heatmap, but with a dendrogram.
backward (
bool
) – Direction of the process.lineages (
Union
[str
,Sequence
[str
],None
]) – Lineages for which to visualize the fate probabilities. IfNone
, use all lineages.cluster_key (
Optional
[str
]) – Key inobs
containing the clusters.clusters (
Union
[str
,Sequence
[str
],None
]) – Clusters to visualize. IfNone
, all clusters will be plotted.basis (
Optional
[str
]) – Basis for scatterplot to use whenmode = 'paga_pie'
. IfNone
, don’t show the scatterplot.cbar (
bool
) – Whether to show colorbar whenmode = 'paga_pie'
.ncols (
Optional
[int
]) – Number of columns whenmode = 'bar'
ormode = 'paga'
.sharey (
bool
) – Whether to share y-axis whenmode = 'bar'
.fmt (
str
) – Format when usingmode = 'heatmap'
ormode = 'clustermap'
.xrot (
float
) – Rotation of the labels on the x-axis.figsize (
Optional
[tuple
[float
,float
]]) – Size of the figure.legend_kwargs (
Mapping
[str
,Any
]) – Keyword arguments forlegend()
. Formode = 'paga_pie'
andbasis = '...'
, this controls the placement of the fate probabilities legend.figsize – Size of the figure.
save (
Union
[Path
,str
,None
]) – Filename where to save the plot.kwargs (
Any
) – Keyword arguments forpaga()
,violin()
orbar()
, depending on themode
.
- Return type:
- Returns:
: Nothing, just plots the figure. Optionally saves it based on
save
.