scripts/plot_files_param_inter.R

In pnojai/rwalk: Random Walk Model of Neurotransmitter Release and Uptake

library(ggplot2)
library(openxlsx)

input_dir <- "./input"           # Input directory, on GitHub
par_dir <- "./scripts"           # File params need a trackable directory

# File parameters, on GitHub
fil_params_all <- read.xlsx(paste(par_dir, "file_params.xlsx", sep = "/"))

fils <- unique(fil_params_all$filename)

fil_not_exists <- sum(!file.exists(paste(input_dir, fils, sep = "/")))
if (fil_not_exists) {stop("Input file not found")}

# Pick a file to work on.
print(fils)
i <- 7

fil_params_cur <- fil_params_all[fil_params_all$filename == fils[i], ]
sample_rate <- head(fil_params_cur$sample_rate, 1) # milliseconds
dat <- read_experiment_csv(paste(input_dir, fils[i], sep = "/"), sr = sample_rate)
# Plot the sweep. Manually save it and view.
qplot(dat$time_sec, dat$electrode, geom = "line")

# Get to work. Repeat this block
fil_params_all <- read.xlsx(paste(par_dir, "file_params.xlsx", sep = "/"))
fil_params_cur <- fil_params_all[fil_params_all$filename == fils[i], ]
dat_list <- list()
max_stim <- max(fil_params_cur$stimulus)
for (stim in fil_params_cur$stimulus) {
        start_idx <- fil_params_cur[stim, "start"]
        if (stim == max_stim) {
                top_row_idx <- nrow(dat)
        } else {
                top_row_idx <- fil_params_cur[(stim + 1), "start"] - 1
        }

        dat_list[[stim]] <- dat[start_idx:top_row_idx, ]
}

# Stimulus number
j <- 10

release <- 3.2
vmax <- 1
km <- 3.5
km

compare_pulse(dat = dat_list[[j]], fil = paste0(fils[i], "_", fil_params_cur[j, "stimulus"]),
              # vmax = fil_params_cur[j, "vmax"],
              vmax = vmax,
              # km = fil_params_cur[j, "km"],
              km = km,
              pulses = fil_params_cur[j, "pulses"],
              pulse_freq = fil_params_cur[j, "pulse_freq"],
              # release = fil_params_cur[j, "release"],
              release = release,
              bin_size = fil_params_cur[j, "bin_size"],
              electrode_distance = fil_params_cur[j, "electrode_distance"],
              dead_space_distance = fil_params_cur[j, "dead_space_distance"],
              diffusion_coefficient = fil_params_cur[j, "diffusion_coefficient"],
              convert_current = fil_params_cur[j, "convert_current"],
              calibration_current = fil_params_cur[j, "calibration_current"],
              calibration_concentration = fil_params_cur[j, "calibration_concentration"],
              fit_region = fil_params_cur[j, "fit_region"],
              base_tolerance = fil_params_cur[j, "base_tolerance"],
              plot_duration_sec = fil_params_cur[j, "plot_duration_sec"])

compare_pulse(dat = dat_list[[j]], fil = paste0(fils[i], "_", fil_params_cur[j, "stimulus"]),
              vmax = fil_params_cur[j, "vmax"],
              # vmax = vmax,
              km = fil_params_cur[j, "km"],
              # km = km,
              pulses = fil_params_cur[j, "pulses"],
              pulse_freq = fil_params_cur[j, "pulse_freq"],
              release = fil_params_cur[j, "release"],
              # release = release,
              bin_size = fil_params_cur[j, "bin_size"],
              electrode_distance = fil_params_cur[j, "electrode_distance"],
              dead_space_distance = fil_params_cur[j, "dead_space_distance"],
              diffusion_coefficient = fil_params_cur[j, "diffusion_coefficient"],
              convert_current = fil_params_cur[j, "convert_current"],
              calibration_current = fil_params_cur[j, "calibration_current"],
              calibration_concentration = fil_params_cur[j, "calibration_concentration"],
              fit_region = fil_params_cur[j, "fit_region"],
              base_tolerance = fil_params_cur[j, "base_tolerance"],
              plot_duration_sec = fil_params_cur[j, "plot_duration_sec"])