idocr: The standard idocr workflow.

In shaliulab/idocr: Analyze traces created in the Individual Drosophila Optogenetics Conditioner (IDOC)

The standard idocr workflow.

Description

Load data from the experiment folder, possibly with some specific settings and return a data frame with the appetitive index of each fly and a plot visualizing the experiment

Usage

idocr(
  experiment_folder,
  treatments = paste0("TREATMENT_", c("A", "B")),
  min_exits_required = 5,
  CSplus_idx = 1,
  border_mm = 5,
  delay = 0,
  src_file = NULL,
  mask_duration = 0.5,
  analysis_mask = NULL,
  n = 20,
  ...
)

Arguments

experiment_folder	Path to folder containing IDOC results .csv files
treatments	Vector of treatments. If named and names contain the word treatment, it is likely that the user is running old API code
min_exits_required	Minimal number of exits to be considered for significance
CSplus_idx	Whether the first treatment (CSplus_idx=1) or the second (CSplus_idx=2) is associated with + exits
border_mm	mm from center of chamber to decision zone edge
delay	Seconds to shift the representation of the treatments on the plot, to account for a latency or lag between treatment delivery start and arrival to behavioral arena
src_file	Path of file to be copied. If NULL, take current file (works on RStudio)
mask_duration	Seconds of behavior to be ignored after last cross, so the same cross is not counted more than once due to noise in the border cross
analysis_mask	Named list of numeric vectors specifying the start and end time in seconds of a period of the experiment that should be analyzed separately
n	Number of channels desired. If less than this amount of animals is found, idocr will make up animals until this amount is hit It (should match nrow x ncol of layout passed in the idocr function)
...	Extra arguments to plot_dataset

Value

tibble

See Also

load_dataset()

preprocess_dataset()

analyse_dataset()

plot_dataset()

export_dataset()

shaliulab/idocr documentation built on June 1, 2025, 4:59 p.m.