dynfeature (version 1.0.1)

calculate_branch_feature_importance: Calculating feature importances across trajectories

Description

Uses the feature importance measures of ranger or caret. calculate_overall_feature_importance calculates the importance for the whole trajectory, calculate_milestone_feature_importance calculates it for individual milestones (e.g. branching points)

Usage

calculate_branch_feature_importance(
  trajectory,
  expression_source = "expression",
  fi_method = fi_ranger_rf_lite(),
  verbose = FALSE
)
calculate_branching_point_feature_importance(
  trajectory,
  expression_source = "expression",
  milestones_oi = trajectory$milestone_ids,
  fi_method = fi_ranger_rf_lite(),
  verbose = FALSE
)
calculate_cell_feature_importance(
  trajectory,
  expression_source = "expression",
  fi_method = fi_ranger_rf_lite(),
  verbose = FALSE
)
calculate_milestone_feature_importance(
  trajectory,
  expression_source = "expression",
  milestones_oi = NULL,
  fi_method = fi_ranger_rf_lite(),
  verbose = FALSE
)
calculate_overall_feature_importance(
  trajectory,
  expression_source = "expression",
  fi_method = fi_ranger_rf_lite(),
  verbose = FALSE
)
calculate_waypoint_feature_importance(
  trajectory,
  expression_source = "expression",
  waypoints = NULL,
  fi_method = fi_ranger_rf_lite(),
  verbose = FALSE
)

Value

A data frame with two or more columns, feature_id, and importance. feature_id is a column in the trajectory expression matrix. Additional columns may be available depending on the function called.

Arguments

trajectory

A trajectory object containing expression values and a trajectory.

expression_source

The expression data matrix, with features as columns.

• If a matrix is provided, it is used as is.

• If a character is provided, trajectory[[expression_source]] should contain the matrix.

• If a function is provided, that function will be called in order to obtain the expression (useful for lazy loading).

fi_method

A feature importance method. Default: fi_ranger_rf_lite(). Check ?fi_methods for a full list of available feature importance methods.

verbose

Whether to print out extra information.

milestones_oi

The milestone(s) for which to calculate feature importance

waypoints

The waypoints, optional

Examples

library(dynwrap)
data(example_trajectory)

calculate_overall_feature_importance(example_trajectory)