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,
  log_abund_detection_thresh,
  delta_log_abund_loss_thresh,
  interval_col,
  q_val,
  log_scale,
  control_ccm = perturbation_ccm,
  control_start_time = start_time,
  control_stop_time = stop_time,
  group_nodes_by,
  newdata = tibble::tibble(),
  nrow,
  size,
  alpha,
  raw_counts
)

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)