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plot_cell_type_perturb_kinetics

Generates a plot to visualize the kinetics of cell type perturbations over time.

plot_cell_type_perturb_kinetics(
  perturbation_ccm,
  cell_groups = NULL,
  start_time = NULL,
  stop_time = NULL,
  interval_step = 1,
  log_abund_detection_thresh = -3,
  delta_log_abund_loss_thresh = 0,
  interval_col = "timepoint",
  q_val = 0.01,
  log_scale = TRUE,
  control_ccm = perturbation_ccm,
  control_start_time = start_time,
  control_stop_time = stop_time,
  group_nodes_by = "cell_type",
  newdata = tibble::tibble(),
  nrow = 1,
  size = 0.75,
  alpha = 0.5,
  raw_counts = FALSE
)

Arguments

  • perturbation_ccm
    CCM object
    A perturbation cell count matrix object.

  • cell_groups
    vector
    Cell groups to include. If NULL, all groups are included.

  • start_time
    numeric
    Start time. If NULL, uses minimum timepoint in data.

  • stop_time
    numeric
    Stop time. If NULL, uses maximum timepoint in data.

  • interval_step
    numeric
    Step size for time intervals.

  • log_abund_detection_thresh
    numeric
    Log abundance detection threshold.

  • delta_log_abund_loss_thresh
    numeric
    Change in log abundance loss threshold.

  • interval_col
    character
    Column name for time intervals.

  • q_val
    numeric
    Q-value threshold for significance.

  • log_scale
    logical
    Use log scale for y-axis.

  • control_ccm
    CCM object
    Control cell count matrix. Defaults to perturbation_ccm.

  • control_start_time
    numeric
    Start time for control interval. Defaults to start_time.

  • control_stop_time
    numeric
    Stop time for control interval. Defaults to stop_time.

  • group_nodes_by
    character
    Column to group nodes by.

  • newdata
    tibble
    New data for predictions.

  • nrow
    integer
    Number of rows in facet wrap.

  • size
    numeric
    Size of points in plot.

  • alpha
    numeric
    Alpha transparency for difference shading.

  • raw_counts
    logical
    Use raw counts.

Value

A ggplot object representing the kinetics of cell type perturbations.

Examples

# Example usage:
plot <- plot_cell_type_perturb_kinetics(perturbation_ccm)
print(plot)