add velocity

Author: zouter

R/6-generate_velocity.R

@@ -14,15 +14,15 @@ add_velocity <- function(
 
   geodesic_distances <- dynwrap::calculate_geodesic_distances(
     trajectory,
-    trajectory$cell_ids,
+    waypoint_cells = trajectory$cell_ids,
     directed = TRUE
   )
 
   cell_id <- first(rownames(trajectory$expression))
   expression_projected <- map(rownames(trajectory$expression), function(cell_id) {
     geodesic_distance <- geodesic_distances[cell_id, ]
 
-    # find closest backwards or frontwards
+    # find closest forwards
     reference_cell_id <- names(which.min(abs(expected_geodesic_difference - geodesic_distance)))
 
     reference_geodesic_difference <- geodesic_distance[reference_cell_id]

R/7-generate_dataset.R

@@ -101,9 +101,12 @@ generate_dataset <- dynutils::inherit_default_params(
     )
 
     # add velocity
-    dataset <- add_velocity(
-      trajectory = dataset
-    )
+    if (add_velocity) {
+      dataset <- add_velocity(
+        trajectory = dataset
+      )
+    }
+
 
     if (add_prior_information) {
       dataset <- dataset %>% dynwrap::add_prior_information(