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make_params

make_params.Rd

Constructs and validates the parameter list used throughout the analysis and plotting pipeline, applying defaults for any unspecified options.

Usage

make_params(
  channels = list(),
  coherence = TRUE,
  network = TRUE,
  normalize_phase = NULL,
  time_res,
  intervals = NULL,
  time_window = FALSE,
  pixel_fct,
  saving = TRUE,
  reload_period = FALSE,
  plotting = list(y_limits_from_previous = TRUE, previous_exp = "path/to/previous/exp",
    override_ranges = FALSE, ranges = list(), plot_types = c("period", "amplitude",
    "RAE", "AUC", "phase", "phase_norm", "3D"), save_format = "svg", colors = list(Ch1 =
    "darkgreen", Ch2 = "purple", Ch3 = "#e5e372", Ch4 = "#00aefe")),
  folder_structure = list(base_dir = "results", interval_dir = "interval", channel_dir =
    "channel")
)

Arguments

channels

A named list of channel definitions. Each element should contain at minimum enabled (logical), label (character), invert (logical), and grid_file (character).

coherence

Logical; whether to compute spatial coherence metrics. Defaults to TRUE.

network

Logical; whether to perform network analysis. Defaults to TRUE.

normalize_phase

Character string naming the channel to use as phase reference for normalisation, or NULL to skip. Defaults to NULL.

time_res

Numeric; the temporal resolution of the data in minutes per frame.

intervals

A named list of numeric vectors of length 2 defining time intervals (start and end in the same units as time_res), or NULL.

time_window

Logical; whether to subset data to defined intervals. Defaults to FALSE.

pixel_fct

Numeric; scaling factor converting pixel units to physical units.

saving

Logical; whether to save outputs to disk. Defaults to TRUE.

reload_period

Logical; whether to reload previously computed period results from cache. Defaults to FALSE.

plotting

A named list of plotting options. See Details.

folder_structure

A named list with element base_dir specifying the root output directory.

Value

A named list of validated analysis parameters, with defaults applied for any unspecified plotting options.

Examples

if (FALSE) { # \dontrun{
params <- make_params(
  channels = list(Ch1 = list(enabled = TRUE, label = "RCaMP",
                             invert = FALSE, grid_file = "ch1.csv")),
  time_res = 30,
  pixel_fct = 0.8
)
} # }