Adds information about treatment and experimental set up to viewr objects for analysis in other pathviewr functions
Usage
insert_treatments(
obj_name,
tunnel_config = "box",
perch_2_vertex = NULL,
vertex_angle = NULL,
tunnel_width = NULL,
tunnel_length = NULL,
stim_param_lat_pos = NULL,
stim_param_lat_neg = NULL,
stim_param_end_pos = NULL,
stim_param_end_neg = NULL,
treatment = NULL
)Arguments
- obj_name
The input viewr object; a tibble or data.frame with attribute
pathviewr_stepsthat includes"viewr"- tunnel_config
The configuration of the experimental tunnel. Currently, pathviewr supports rectangular "box" and V-shaped tunnel configurations.
- perch_2_vertex
If using a V-shaped tunnel, this is the vertical distance between the vertex and the height of the perches. If the tunnel does not have perches, insert the vertical distance between the vertex and the height of the origin (0,0,0).
- vertex_angle
If using a V-shaped tunnel, the angle of the vertex (in degrees)
vertex_angledefaults to 90.- tunnel_width
If using a box-shaped tunnel, the width of the tunnel.
- tunnel_length
The length of the tunnel.
- stim_param_lat_pos
The size of the stimulus on the lateral positive wall of the tunnel. Eg. for 10cm wide gratings,
stim_param_lat_pos= 0.1.- stim_param_lat_neg
The size of the stimulus on the lateral negative wall of the tunnel..
- stim_param_end_pos
The size of the stimulus on the end positive wall of the tunnel.
- stim_param_end_neg
The size of the stimulus on the end negative wall of the tunnel.
- treatment
The name of the treatment assigned to all rows of the viewr object. Currently only able to accept a single treatment per viewr data object.
Value
A viewr object (tibble or data.frame with attribute
pathviewr_steps that includes "treatments added"). Depending
on the argument tunnel_config, the viewr object also includes
columns storing the values of the supplied arguments. This experimental
information is also stored in the viewr object's metadata
See also
Other utility functions:
clean_by_span(),
remove_duplicate_frames(),
remove_vel_anomalies(),
set_traj_frametime()
Examples
## Import sample data from package
motive_data <-
read_motive_csv(system.file("extdata", "pathviewr_motive_example_data.csv",
package = 'pathviewr'))
flydra_data <-
read_flydra_mat(system.file("extdata", "pathviewr_flydra_example_data.mat",
package = 'pathviewr'),
subject_name = "birdie_sanders")
## Clean data up to and including get_full_trajectories()
motive_data_full <-
motive_data %>%
relabel_viewr_axes() %>%
gather_tunnel_data() %>%
trim_tunnel_outliers() %>%
rotate_tunnel() %>%
select_x_percent(desired_percent = 50) %>%
separate_trajectories(max_frame_gap = "autodetect") %>%
get_full_trajectories(span = 0.95)
#> autodetect is an experimental feature -- please report issues.
flydra_data_full <-
flydra_data %>%
redefine_tunnel_center(length_method = "middle",
height_method = "user-defined",
height_zero = 1.44) %>%
select_x_percent(desired_percent = 50) %>%
separate_trajectories(max_frame_gap = "autodetect") %>%
get_full_trajectories(span = 0.95)
#> autodetect is an experimental feature -- please report issues.
## Now add information about the experimental configuration. In this example,
## a V-shaped tunnel in which the vertex is 90deg and lies 0.40m below the
## origin. The visual stimuli on the lateral and end walls have a cycle
## length of 0.1m and 0.3m respectively, and the treatment is labeled
## "lat10_end30"
motive_v <-
motive_data_full %>%
insert_treatments(tunnel_config = "v",
perch_2_vertex = 0.4,
vertex_angle = 90,
tunnel_length = 2,
stim_param_lat_pos = 0.1,
stim_param_lat_neg = 0.1,
stim_param_end_pos = 0.3,
stim_param_end_neg = 0.3,
treatment = "lat10_end_30")
# For an experiment using the box-shaped configuration where the tunnel is 1m
# wide and 3m long and the visual stimuli on the lateral and end walls have a
# cycle length of 0.2 and 0.3m, respectively, and the treatment is labeled
# "lat20_end30".
flydra_box <-
flydra_data_full %>%
insert_treatments(tunnel_config = "box",
tunnel_width = 1,
tunnel_length = 3,
stim_param_lat_pos = 0.2,
stim_param_lat_neg = 0.2,
stim_param_end_pos = 0.3,
stim_param_end_neg = 0.3,
treatment = "lat20_end30")
## Check out the new columns in the resulting objects
names(motive_v)
#> [1] "tunnel_config" "perch_2_vertex" "vertex_angle"
#> [4] "tunnel_length" "stim_param_lat_pos" "stim_param_lat_neg"
#> [7] "stim_param_end_pos" "stim_param_end_neg" "treatment"
#> [10] "frame" "time_sec" "subject"
#> [13] "position_length" "position_width" "position_height"
#> [16] "rotation_length" "rotation_width" "rotation_height"
#> [19] "rotation_real" "mean_marker_error" "traj_id"
#> [22] "file_sub_traj" "traj_length" "start_length"
#> [25] "end_length" "length_diff" "start_length_sign"
#> [28] "end_length_sign" "direction"
names(flydra_box)
#> [1] "tunnel_config" "tunnel_width" "tunnel_length"
#> [4] "stim_param_lat_pos" "stim_param_lat_neg" "stim_param_end_pos"
#> [7] "stim_param_end_neg" "treatment" "frame"
#> [10] "time_sec" "subject" "position_length"
#> [13] "position_width" "position_height" "velocity"
#> [16] "length_inst_vel" "width_inst_vel" "height_inst_vel"
#> [19] "traj_id" "file_sub_traj" "traj_length"
#> [22] "start_length" "end_length" "length_diff"
#> [25] "start_length_sign" "end_length_sign" "direction"