stereo.algorithm.time_series_analysis.TimeSeriesAnalysis.main#
- TimeSeriesAnalysis.main(run_method='tvg_marker', use_col='timepoint', branch=None, p_val_combination='FDR', cluster_number=6, **kwargs)[source]#
- Parameters:
run_method – the model type when the algorithm is run, default =
tvg_marker
.tvg_marker
: Calculate time variable gene based on expression of celltypes in branchother
: Use fuzzy C means cluster method to cluster genes based on 1-p_value of celltypes in branchuse_col – the col in obs representing celltype or clustering
branch – celltypes order in use_col
p_val_combination – p_value combination method to use, choosing from [‘fisher’, ‘mean’, ‘FDR’]
cluster_number – number of cluster
Note
All the parameters below are key word arguments and only for
other
run_method.- Parameters:
spatial_weight – the weight to combine spatial feature, defaults to 1.
n_spatial_feature – n top features to combine of spatial feature, defaults to 2.
temporal_mean_threshold – filter out genes of which mean absolute temporal feature <= temporal_mean_threshold, defaults to 0.85.
temporal_top_threshold – filter out genes of which top absolute temporal feature < temporal_top_threshold, defaults to 1.
Epsilon – max value to finish iteration, defaults to 1e-7.
w_size – window size to rasterizing spatial expression, default to 20.
use_col – the col in obs representing celltype or clustering, default to None.
branch – celltypes order in use_col, default to None.