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Run WOT analysis

Source: R/RunWOT.R
RunWOT.Rd

Run WOT analysis

Usage

RunWOT(
  srt = NULL,
  assay_x = "RNA",
  layer_x = "counts",
  assay_y = c("spliced", "unspliced"),
  layer_y = "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 = FALSE,
  save_plot = FALSE,
  plot_format = c("pdf", "png", "svg"),
  plot_dpi = 300,
  plot_prefix = "wot",
  dirpath = "./",
  return_seurat = !is.null(srt),
  verbose = TRUE
)

Arguments

srt

A Seurat object. Default is NULL. If provided, adata will be ignored.

assay_x

Assay to convert in the anndata object.

layer_x

Layer name for assay_x in the Seurat object.

assay_y

Assay to convert in the anndata object.

layer_y

Layer names for the assay_y in the Seurat object.

adata

An anndata object. Default is NULL.

group.by

Name of one or more meta.data columns to group (color) cells by.

time_field

A character string specifying the column name in adata.obs or srt@meta.data that contains the time information.

growth_iters

A 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

The starting time point for trajectory and fate analysis.

time_to

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

Whether to compute and store the coupling matrix between the specified time_from and time_to. Default is FALSE.

recalculate

Whether to recalculate the transport maps even if they already exist at the specified tmap_out location. Default is FALSE.

palette

Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "Paired".

palcolor

Custom colors used to create a color palette. Default is NULL.

show_plot

Whether to show the plot. Default is FALSE.

save_plot

Whether to save plots to files. Default is FALSE.

plot_format

Format for saved plots: "png" (default), "pdf", or "svg".

plot_dpi

Resolution (DPI) for saved plots. Default is 300.

plot_prefix

Prefix for saved plot filenames. Default is "cellrank".

dirpath

The directory to save the plots. Default is "./cellrank".

return_seurat

Whether to return a Seurat object instead of an anndata object. Default is TRUE.

verbose

Whether to print the message. Default is TRUE.

References

Geoffrey et al. (2019) Cell, GitHub

See also

srt_to_adata

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunSlingshot(
  pancreas_sub,
  group.by = "SubCellType",
  reduction = "UMAP"
)

print(range(pancreas_sub$Lineage1, na.rm = TRUE))

pancreas_sub <- RunWOT(
  pancreas_sub,
  group.by = "SubCellType",
  time_field = "Lineage1",
  time_from = min(pancreas_sub$Lineage1, na.rm = TRUE),
  time_to = max(pancreas_sub$Lineage1, na.rm = TRUE),
  get_coupling = TRUE,
  tmap_out = "tmaps/lineage_tmap"
)

pancreas_sub$Custom_Time <- sample(
  1:10,
  ncol(pancreas_sub),
  replace = TRUE
)
pancreas_sub <- RunWOT(
  pancreas_sub,
  group.by = "CellType",
  time_field = "Custom_Time",
  time_from = 1,
  time_to = 10,
  tmap_out = "tmaps/custom_tmap"
)
} # }