Run WOT analysis
Usage
RunWOT(
srt = NULL,
assay_X = "RNA",
slot_X = "counts",
assay_layers = c("spliced", "unspliced"),
slot_layers = "counts",
adata = NULL,
group_by = NULL,
time_field = "Time",
growth_iters = 3L,
tmap_out = "tmaps/tmap_out",
time_from = NULL,
time_to = NULL,
get_coupling = FALSE,
recalculate = FALSE,
palette = "Paired",
palcolor = NULL,
show_plot = TRUE,
save = FALSE,
dpi = 300,
dirpath = "./",
fileprefix = "",
return_seurat = !is.null(srt)
)Arguments
- srt
A Seurat object.
- assay_X
Assay to convert as the main data matrix (X) in the anndata object.
- slot_X
Slot name for assay_X in the Seurat object.
- assay_layers
Assays to convert as layers in the anndata object.
- slot_layers
Slot names for the assay_layers in the Seurat object.
- adata
An anndata object.
- group_by
Variable to use for grouping cells in the Seurat object.
- time_field
A character string specifying the column name in `adata.obs` or `srt@meta.data` that contains the time information.
- growth_iters
An integer specifying the number of growth iterations to perform during the OT Model computation. Default is 3.
- tmap_out
A character string specifying the path to store the computed transport maps.
- time_from
A numeric value specifying the starting time point for trajectory and fate analysis.
- time_to
A numeric value specifying the ending time point for trajectory and fate analysis. If not provided, only trajectory and fate analysis for the specified `time_from` will be performed.
- get_coupling
A logical value indicating whether to compute and store the coupling matrix between the specified `time_from` and `time_to`. Default is FALSE.
- recalculate
A logical value indicating whether to recalculate the transport maps even if they already exist at the specified `tmap_out` location. Default is FALSE.
- palette
The palette to use for coloring cells.
- palcolor
A vector of colors to use as the palette.
- show_plot
Whether to show the PAGA plot.
- save
Whether to save the PAGA plots.
- dpi
The DPI (dots per inch) for saving the PAGA plot.
- dirpath
The directory to save the PAGA plots.
- fileprefix
The file prefix to use for the PAGA plots.
- return_seurat
Whether to return a Seurat object instead of an anndata object. Default is TRUE.