data-raw/example_dataset.R

In dynverse/dynwrap: Representing and Inferring Single-Cell Trajectories

library(tidyverse)
library(dynwrap)

set.seed(1)

ncells <- 500
pseudotime <- runif(ncells)

expression <- matrix(
  c(
    pseudotime,
    (.5 - pseudotime) ** 2,
    sqrt(20 - pseudotime * 2)
  ),
  ncol = 3,
  dimnames = list(as.character(rep(seq_len(ncells))), as.character(c("A", "B", "C")))
)
expression <- expression + rnorm(length(expression), sd = 0.02)

names(pseudotime) <- rownames(expression) <- paste0("Cell", seq_len(nrow(expression)))

start_id <- rownames(expression)[which.min(pseudotime)]

counts <- round(expression)

example_dataset <-
  wrap_data(
    id = "example",
    cell_ids = rownames(counts)
  ) %>%
  add_expression(
    expression = expression,
    counts = counts
  ) %>%
  add_dimred(
    dimred = expression
  )

example_trajectory <- example_dataset %>%
  add_linear_trajectory(
    pseudotime = pseudotime,
    directed = TRUE
  ) %>%
  add_prior_information() %>%
  add_cell_waypoints() %>%
  add_dimred(dimred = expression)

dynplot::plot_graph(example_trajectory)
dynplot::plot_dimred(example_trajectory)
dynplot::plot_heatmap(example_trajectory)
dynplot::plot_dimred(dynwrap::example_trajectory, "feature", feature_oi = "C")

usethis::use_data(example_trajectory, overwrite = TRUE)
usethis::use_data(example_dataset, overwrite = TRUE)