eyeris (version 2.0.0)

plot.eyeris: Plot pre-processed pupil data from eyeris

Description

S3 plotting method for objects of class eyeris. Plots a single-panel timeseries for a subset of the pupil timeseries at each preprocessing step. The intended use of this function is to provide a simple method for qualitatively assessing the consequences of the preprocessing recipe and parameters on the raw pupillary signal.

Usage

# S3 method for eyeris
plot(
  x,
  ...,
  steps = NULL,
  preview_n = NULL,
  preview_duration = NULL,
  preview_window = NULL,
  seed = NULL,
  block = 1,
  plot_distributions = FALSE,
  suppress_prompt = TRUE,
  verbose = TRUE,
  add_progressive_summary = FALSE,
  num_previews = deprecated()
)

Value

No return value; iteratively plots a subset of the pupil timeseries from each preprocessing step run

Arguments

x

An object of class eyeris derived from load_asc()

...

Additional arguments to be passed to plot

steps

Which steps to plot; defaults to all (i.e., plot all steps). Otherwise, pass in a vector containing the index of the step(s) you want to plot, with index 1 being the original raw pupil timeseries

preview_n

Number of random example "epochs" to generate for previewing the effect of each preprocessing step on the pupil timeseries

preview_duration

Time in seconds of each randomly selected preview

preview_window

The start and stop raw timestamps used to subset the preprocessed data from each step of the eyeris workflow for visualization Defaults to NULL, meaning random epochs as defined by preview_n and preview_duration will be plotted. To override the random epochs, set preview_window here to a vector with relative start and stop times (in seconds), for example -- c(5,6) -- to indicate the raw data from 5-6 secs on data that were recorded at 1000 Hz). Note, the start/stop time values indicated here are in seconds because eyeris automatically computes the indices for the supplied range of seconds using the $info$sample.rate metadata in the eyeris S3 class object

seed

Random seed for current plotting session. Leave NULL to select preview_n number of random preview "epochs" (of preview_duration) each time. Otherwise, choose any seed-integer as you would normally select for base::set.seed(), and you will be able to continue re-plotting the same random example pupil epochs each time -- which is helpful when adjusting parameters within and across eyeris workflow steps

block

For multi-block recordings, specifies which block to plot. Defaults to 1. When a single .asc data file contains multiple recording blocks, this parameter determines which block's timeseries to visualize. Must be a positive integer not exceeding the total number of blocks in the recording

plot_distributions

Logical flag to indicate whether to plot both diagnostic pupil timeseries and accompanying histograms of the pupil samples at each processing step. Defaults to FALSE

suppress_prompt

Logical flag to disable interactive confirmation prompts during plotting. Defaults to TRUE, which avoids hanging behavior in non-interactive or automated contexts (e.g., RMarkdown, scripts) Set to FALSE only when running inside glassbox() with interactive_preview = TRUE, where prompting after each step is desired, as well as in the generation of interactive HTML reports with bidsify

verbose

A logical flag to indicate whether to print status messages to the console. Defaults to TRUE. Set to FALSE to suppress messages about the current processing step and run silently

add_progressive_summary

Logical flag to indicate whether to add a progressive summary plot after plotting. Defaults to FALSE. Set to TRUE to enable the progressive summary plot (useful for interactive exploration). Set to FALSE to disable the progressive summary plot (useful in automated contexts like bidsify reports)

num_previews

(Deprecated) Use preview_n instead

See Also

lifecycle::deprecate_warn()

Examples

# first, generate the preprocessed pupil data
my_eyeris_data <- system.file("extdata", "memory.asc", package = "eyeris") |>
  eyeris::load_asc() |>
  eyeris::deblink(extend = 50) |>
  eyeris::detransient() |>
  eyeris::interpolate() |>
  eyeris::lpfilt(plot_freqz = TRUE) |>
  eyeris::zscore()

# controlling the timeseries range (i.e., preview window) in your plots:

## example 1: using the default 10000 to 20000 ms time subset
plot(my_eyeris_data, seed = 0, add_progressive_summary = TRUE)

## example 2: using a custom time subset (i.e., 1 to 500 ms)
plot(
  my_eyeris_data,
  preview_window = c(0.01, 0.5),
  seed = 0,
  add_progressive_summary = TRUE
)

# controlling which block of data you would like to plot:

## example 1: plots first block (default)
plot(my_eyeris_data, seed = 0)

## example 2: plots a specific block
plot(my_eyeris_data, block = 1, seed = 0)

## example 3: plots a specific block along with a custom preview window
##   (i.e., 1000 to 2000 ms)
plot(
  my_eyeris_data,
  block = 1,
  preview_window = c(1, 2),
  seed = 0
)