cycle_over_time: Plot cycle score over pseudotime
In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Plot cycle score over pseudotime

cycle_over_time(
  plot_data,
  color_by,
  time_col,
  sel_phase = c("M", "S"),
  num_col = 1,
  extend_max = 0.4,
  AP = NULL
)

`plot_data`	a dataframe with cell cycle scores and pseudotime information
`color_by`	which column to color
`time_col`	where the pseudotime information is stored
`sel_phase`	which cell cycle phases to display, can be M, M.G1, G1.S, S, G2.M
`num_col`	in how many columns the subplots are arranged

exp_mat_cc <- as.matrix (GetAssayData (all_data, assay='RNA', slot='data'))
ans <- get_phase_score (exp_mat_cc)
plot_data <- cbind (ans, all_data@meta.data)
cycle_over_time (plot_data, time_col='MGP_PT')