scFates.pl.trends

scFates.pl.trends(adata, features=None, cluster=None, highlight_features='A', n_features=10, root_milestone=None, milestones=None, module=None, branch=None, annot=None, title='', feature_cmap='RdBu_r', pseudo_cmap='viridis', plot_emb=True, plot_heatmap=True, wspace=None, show_segs=True, basis=None, heatmap_space=0.5, offset_names=0.15, fontsize=9, style='normal', ordering='pearson', ord_thre=0.7, figsize=None, axemb=None, show=None, output_mean=False, save=None, return_genes=None, **kwargs)

Plot a set of fitted features over pseudotime.

Parameters:

adata AnnData

Annotated data matrix.

features default: None

Name of the fitted features.

highlight_features Union[List, Literal['A', 'fdr']] (default: 'A')

which features will be annotated on the heatmap, by default, features with highest amplitude are shown.

n_features int (default: 10)

number of top features to show if no list are provided.

root_milestone Optional[str] (default: None)

tip defining progenitor branch.

milestones Optional[str] (default: None)

tips defining the progenies branches.

module Optional[Literal['early', 'late']] (default: None)

if bifurcation analysis as been performed, subset features to a specific module.

branch Optional[str] (default: None)

if bifurcation analysis as been performed, subset features to a specific milestone.

annot Optional[str] (default: None)

adds an annotation row on top of the heatmap.

title str (default: '')

add a title.

feature_cmap str (default: 'RdBu_r')

colormap for features.

pseudo_cmap str (default: 'viridis')

colormap for pseudotime.

plot_emb bool (default: True)

call pl.trajectory on the left side.

plot_heatmap bool (default: True)

show heatmap on the right side.

wspace Optional[float] (default: None)

width space between emb and heatmap.

show_segs bool (default: True)

display segments on emb.

basis Optional[str] (default: None)

Name of the obsm basis to use if plot_emb is True.

heatmap_space float (default: 0.5)

how much space does the heatmap take, in proportion of the whole plot space.

offset_names float (default: 0.15)

how far on the right the annotated features should be displayed, in proportion of the heatmap space.

fontsize int (default: 9)

font size of the feature annotations.

style Literal['normal', 'italic', 'oblique'] (default: 'normal')

font style.

ordering Optional[Literal['pearson', 'spearman', 'quantile', 'max']] (default: 'pearson')

strategy to order the features on heatmap, quantile takes the mean pseudotime of the choosen value.

ord_thre default: 0.7

for ‘max’: proportion of maximum of fitted value to consider to compute the mean pseudotime. for ‘quantile’: quantile to consider to compute the mean pseudotime. for ‘pearson’/’spearman’: proportion of max value to assign starting cell.

figsize Optional[tuple] (default: None)

figure size.

axemb default: None

existing ax for plotting emb

output_mean bool (default: False)

output mean fitted values to adata.

show Optional[bool] (default: None)

show the plot.

save Union[str, bool, None] (default: None)

save the plot.

return_genes Optional[bool] (default: None)

return list of genes following the order displayed on the heatmap.

**kwargs

if plot_emb=True, arguments passed to scFates.pl.trajectory() or scFates.pl.dendrogram() if basis=”dendro”

Returns:

If show==False a matrix of Axes