Reconstruct cell state lineage trajectories

See carving cell trajectories vignette.

Arguments

gene_modules_name	character string. The name of the list of gene modules whose weights will be optimized by this method.
optim_strategy	character string. Specifies the algorithm used to optimize the gene module weights. Either "SA" for simulated annealing (default) or "GA" for genetic algorithm. Different processing plots will be generated depending of the selected strategy.
optim_objectives	a character vector containing a subset of of either: 'timecorr' to favor a population of candidate cell lineages maximizing their Spearman correlation with the 'timepoint' phenotypic metadata. 'complexity' to favor a population of candidate cell lineages minimizing the number of leaves of the reconstructed tree. 'smoothness' to favor a population of candidate cell lineages minimizing the irregularity of the gene expression pattern along the differentiation trajectories. Multiple elements can be specified if the optimization strategy is set to 'GA' but a single one 'SA'. Default to c('timecorr').
GA_selection_objectives	character vector. If 'GA' is selected as optimization strategy, the final objectives used to select the optimal cell lineage. Any of the optim_objectives options can be selected. If more than one objective is specified, the geometric average of these objectives will be used to select the optimal solution. Default to "timecorr".
GA_num_generations	integer value. If 'GA' is selected as optimization strategy, the number of generation of the genetic algorithm. Default to 200.
GA_pop_size	integer value. If 'GA' is selected as optimization strategy, the size of population of the genetic algorithm. Default to 200.
SA_control	List. If 'SA' is selected as optimization strategy, the list controlling the simulated annealing algorithm behavior. See documentation of the underlying GeneSA function.
SA_maxit	interger value, the maximum number of iteration of the simulated annealing algorithm. Default to 500.
cluster_size_limit	integer value. The maximum cell cluster size. If NULL (default) the cluster_size_limit_ratio argument is used instead.
cluster_size_limit_ratio	numeric value. Specifies the maximum cell cluster size as a ratio of the total number of cells. Default to 0.02.
clustering_timepoint_first	logical. Whether to pre-cluster the cells by 'timepoint' or not (default).
canalize	logical. Whether to constraint the cell state graph using a gaussian kernel obtained from the optimal cluster level graph. Default to TRUE.
kernel_sigma	numeric value. Defines the standard deviation of the gaussian kernel used to canalize the trajectories. Default to 1.
allow_multiple_roots	(Experimental) logical. Whether to allow reconstructed cell lineages to start from multiple root states. Default to FALSE.
output_name	character string. The name of the directory storing the processing plots. This directory will be created in the Antler's object output directory.
cell_colors	character string. The name of the phenotypic metadata to show on the cell state graph plots. Default to 'cells_samples'.
seed	integer value. Set the random number generator seed for reproducibility.