R/beh_mat_tidy.R

In SenguptaLab/MF.matR: Takes mirofluidics data and does stuff with it

#' beh_mat_tidy
#' Takes a matlab behmat file and converts it to long format
#' plus it assigns binary state columns to each behavioral state class
#' @param bins number of time frames to bin. generally 400 for 20 minute video is standard
#' @param frames number of frames in the video
#' @export
#' @examples
#' beh_mat_tidy


beh_mat_tidy <- function(bins, frames, interactive = TRUE, folder = folder) {
  if(interactive) {
    message("Choose behmat file")
    behmat<-readr::read_csv(file.choose(), col_names = FALSE)
    message("Choose ExpInfo file")
    ExpInfo <- readr::read_csv(file.choose(), col_names = TRUE)
  } else {
    behPath <- fs::dir_ls(folder, regex = "behmat")
    ExpInfoPath <- fs::dir_ls(folder, regex = "Expinfo")
    message("reading behmat file")
    behmat <- readr::read_csv(behPath, col_names = FALSE)
    ExpInfo <- readr::read_csv(ExpInfoPath, col_names = TRUE)
    return(message("file reading complete"))
  }

  behmat<- ExpInfo %>%
    mutate(date = factor(date)) %>%
      expand_grid(., behmat) %>%
    mutate(worm = factor(seq(1:nrow(behmat))))
  behmat <- behmat %>% tidyr::gather(key = "time",
                           value = "state",
                           tidyselect::starts_with("X")) %>% #put all data columns (time = "t1 ... "t2400") into long format
   dplyr::mutate(time = as.numeric(gsub("[^0-9]", "", time)),
                 wormID = interaction(date, genotype, experimentNum, stimulus, condition, worm),
                 state_name = dplyr::case_when(
    #!state %in% c(1:8) ~ "NA",
    state == "1" ~ "Forward",
    state == "2" ~ "Curve",
    state == "3" ~ "Reverse",
    state == "4" ~ "Pause",
    state == "5" ~ "Omega-R",
    state == "6" ~ "Omega-F",
    state %in% c("7", "8") ~ "no_state_call",
    TRUE ~ "NA"
  )
)
}