pathviewr (version 1.1.8)

separate_trajectories: Separate rows of data into separately labeled trajectories.

Description

Separate rows of data into separately labeled trajectories.

Usage

separate_trajectories(
  obj_name,
  max_frame_gap = 1,
  frame_rate_proportion = 0.1,
  frame_gap_messaging = FALSE,
  frame_gap_plotting = FALSE,
  ...
)

Value

A viewr object (tibble or data.frame with attribute pathviewr_steps that includes "viewr") in which a new column file_sub_traj is added, which labels trajectories within the data by concatenating file name, subject name, and a trajectory number (all separated by underscores).

Arguments

obj_name

The input viewr object; a tibble or data.frame with attribute pathviewr_steps that includes "viewr"

max_frame_gap

Default 1; defines the largest permissible gap in data before a new trajectory is forced to be defined. Can be either a numeric value or "autodetect". See Details for more.

frame_rate_proportion

Default 0.10; if max_frame_gap = "autodetect", proportion of frame rate to be used as a reference (see Details).

frame_gap_messaging

Default FALSE; should frame gaps be reported in the console?

frame_gap_plotting

Default FALSE; should frame gap diagnostic plots be shown?

...

Additional arguments passed to/from other pathviewr functions

Author

Vikram B. Baliga and Melissa S. Armstrong

Details

This function is designed to separate rows of data into separately labeled trajectories.

The max_frame_gap parameter determines how trajectories will be separated. If numeric, the function uses the supplied value as the largest permissible gap in frames before a new trajectory is defined.

If max_frame_gap = "autodetect" is used, the function attempts to guesstimate the best value(s) of max_frame_gap. This is performed separately for each subject in the data set, i.e. as many max_frame_gap values will be estimated as there are unique subjects. The highest possible value of any max_frame_gap is first set as a proportion of the capture frame rate, as defined by the frame_rate_proportion parameter (default 0.10). For each subject, a plot of total trajectory counts vs. max frame gap values is created internally (but can be plotted via setting frame_gap_plotting = TRUE). As larger max frame gaps are allowed, trajectory count will necessarily decrease but may reach a value that likely represents the "best" option. The "elbow" of that plot is then used to find an estimate of the best max frame gap value to use.

See Also

Other data cleaning functions: gather_tunnel_data(), get_full_trajectories(), quick_separate_trajectories(), redefine_tunnel_center(), relabel_viewr_axes(), rename_viewr_characters(), rotate_tunnel(), select_x_percent(), standardize_tunnel(), trim_tunnel_outliers(), visualize_frame_gap_choice()

Other functions that define or clean trajectories: get_full_trajectories(), quick_separate_trajectories(), visualize_frame_gap_choice()

Examples

## Import the example Motive data included in the package
motive_data <-
  read_motive_csv(system.file("extdata", "pathviewr_motive_example_data.csv",
                              package = 'pathviewr'))

## Clean the file. It is generally recommended to clean up to the
## "select" step before running select_x_percent().
motive_selected <-
  motive_data %>%
  relabel_viewr_axes() %>%
  gather_tunnel_data() %>%
  trim_tunnel_outliers() %>%
  rotate_tunnel() %>%
  select_x_percent(desired_percent = 50)

## Now separate trajectories using autodetect
motive_separated <-
  motive_selected %>%
  separate_trajectories(max_frame_gap = "autodetect",
                        frame_rate_proportion = 0.1)

## See new column file_sub_traj for trajectory labeling
names(motive_separated)