inst/extdata/single_fly/script.R

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

library(idocrdev)

##############################################
# CHANGE CODE BELOW THIS LINE
##############################################

#### Probably you want to change this

# Supply an experiment contained in the working directory
# Press TAB to autocomplete
experiment_folder <- "inst/extdata/real2/"

# Change what treatment A and B are
# to fit it to your needs
treatment_A <- "OCT"
treatment_B <- "MCH+ES"

# leave this empty or fill something relevant for the experiment
# it will appear in the subtitle of the plot
# (below the big title)
description <- "Enter a description here"

# Minimal number of exits required to consider the data
# of one animal significant and then compute a index from it
min_exits_required <- 3

# Apply a time offset to the treatment time series
# to account for the time it takes for odour to
# arrive to the chambers
# Units in seconds
delay <- 0


#### Probably you dont want to change this
#### Please change these numbers only if you know what you are doing

# Define a distance from the center of the chamber
# to the decision zone
# Units in mm
border_mm <- 5

# Behavioral masking
# Ignore exits happening this amount of seconds
# after the previous exit
# to avoid counting the same exit 
# as two exits happening within ridiculously little time  
mask_duration <- 0.5


paradigm_name <- "DUMMY"

# this is whatever
analysis_mask_list <- list(
  DUMMY = c(0, Inf),
  PARADIGM_A = list(PRE1 = c(1, 3)),#, TEST = c(6, 8)),
  PARADIGM_B = list(PRE1 = c(1, 3), TEST = c(6, 8))
)

analysis_mask <- analysis_mask_list[[paradigm_name]] * 60
     
##################################################
# CAUTION!! DONT CHANGE ANY CODE BELOW THIS LINE
##################################################

treatments <- c(
  TREATMENT_A = treatment_A,
  TREATMENT_B = treatment_B
)

src_file <- rstudioapi::getActiveDocumentContext()$path

p1 <- idocr(experiment_folder = experiment_folder,
            treatments = treatments,
            border_mm = border_mm,
            min_exits_required = min_exits_required,
            src_file = src_file,
            subtitle = description,
            delay = delay,
            mask_duration = mask_duration,
            plot_mask = c(0 , 4) * 60
            # analysis_mask = analysis_mask
            )

export_summary(experiment_folder = experiment_folder)