scripts/stim_df_analysis_wightman_demo.R
In pnojai/rwalk: Random Walk Model of Neurotransmitter Release and Uptake
library(ggplot2)
library(dplyr)
library(data.table)
# Maha's inputs as of 7/30/2019
# Global variables
pipeline_dir <- "./pipeline"
input_dir <- paste(pipeline_dir, "06_Library", sep = "/")# WT - Pre-AMPH
dat_fil <- "stim_df.csv"
stim_df <- fread(paste(input_dir, dat_fil, sep = "/"))
# WT - Pre-AMPH
dat_merge_wt_pre <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "wt" & stimulus >= 1 & stimulus <= 3 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_wt_pre <- rename(dat_merge_wt_pre, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_wt_pre$time_sec, dat_merge_wt_pre$electrode, geom = "line")
# WT - AMPH_06_10
dat_merge_wt_amph_0610 <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "wt" & stimulus >= 6 & stimulus <= 10 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_wt_amph_0610 <- rename(dat_merge_wt_amph_0610, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_wt_amph_0610$time_sec, dat_merge_wt_amph_0610$electrode, geom = "line")
# WT - AMPH_16_20
dat_merge_wt_amph_1620 <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "wt" & stimulus >= 16 & stimulus <= 20 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_wt_amph_1620 <- rename(dat_merge_wt_amph_1620, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_wt_amph_1620$time_sec, dat_merge_wt_amph_1620$electrode, geom = "line")
# KO - Pre-AMPH
dat_merge_ko_pre <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "ko" & stimulus >= 1 & stimulus <= 3 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_ko_pre <- rename(dat_merge_ko_pre, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_ko_pre$time_sec, dat_merge_ko_pre$electrode, geom = "line")
dat_merge_ko_pre <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "ko" & stimulus >= 1 & stimulus <= 3 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_ko_pre <- rename(dat_merge_ko_pre, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_ko_pre$time_sec, dat_merge_ko_pre$electrode, geom = "line")
# KO - AMPH_06_10
dat_merge_ko_amph_0610 <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "ko" & stimulus >= 6 & stimulus <= 10 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_ko_amph_0610 <- rename(dat_merge_ko_amph_0610, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_ko_amph_0610$time_sec, dat_merge_ko_amph_0610$electrode, geom = "line")
# unique(select(stim_df, animal, genotype, include) %>%
# filter(genotype == "ko" & include == TRUE))
#
# dat_merge_ko_amph_0610 <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
# filter(animal == 1905302 & genotype == "ko" & stimulus >= 8 & stimulus <= 8 & include == TRUE & stim_time_sec <= 120) %>%
# group_by(stim_time_sec) %>%
# summarize(mean(electrode_concentration))
# dat_merge_ko_amph_0610 <- rename(dat_merge_ko_amph_0610, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
# qplot(dat_merge_ko_amph_0610$time_sec, dat_merge_ko_amph_0610$electrode, geom = "line")
# Find the extra peak
# KO - AMPH_16_20
dat_merge_ko_amph_1620 <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "wt" & stimulus >= 16 & stimulus <= 20 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_ko_amph_1620 <- rename(dat_merge_ko_amph_1620, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_ko_amph_1620$time_sec, dat_merge_ko_amph_1620$electrode, geom = "line")
# Plot and compile results.
results <- data.frame(genotype = character(),
amphetamine = character(),
release = double(),
vmax = double(),
km = double(),
stringsAsFactors = FALSE)
# Constants
pulses <- 30
pulse_freq <- 50
bin_size <- 2.0
electrode_distance <- 1000
dead_space_distance <- 4
diffusion_coefficient <- 2.7 * 10^-6
convert_current <- FALSE
fit_region = "fall"
# WT - Pre-AMPH
# Maha: 7/30
# Variables
genotype <- "WT"
amphetamine <- "PRE"
release <- 1.8
vmax <- 4.8
km <- 5
base_tolerance <- 0.125
plot_duration_sec = 5
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_wt_pre, fil = "Wild Type - Pre-AMPH",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# WT - Post-AMPH 6-10
# Variables
genotype <- "WT"
amphetamine <- "POST_06-10"
release <- 5.75
vmax <- 4.8
km <- 26
base_tolerance <- 0.5
plot_duration_sec = 25
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_wt_amph_0610, fil = "Wild Type - Post-AMPH 06-10",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# WT - Post-AMPH 16-20
# Variables
genotype <- "WT"
amphetamine <- "POST_16-20"
release <- 4.2
vmax <- 4.8
km <- 32
base_tolerance <- 0.05
plot_duration_sec = 50
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_wt_amph_1620, fil = "Wild Type - Post-AMPH 16-20",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# ----------------- END OF WILD TYPE -----------------#
# ----------------- BEGIN KNOCKOUT -----------------#
# KO - Pre-AMPH
# Variables
genotype <- "KO"
amphetamine <- "PRE"
release <- 1.8
vmax <- 4.8
km <- 5
base_tolerance <- 0.05
plot_duration_sec = 10
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_ko_pre, fil = "Knockout - Pre-AMPH",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# KO - Post-AMPH 6-10
# Variables
genotype <- "KO"
amphetamine <- "POST_06-10"
release <- 4.1
vmax <- 4.8
km <- 26
base_tolerance <- 0.12
plot_duration_sec = 30
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_ko_amph_0610, fil = "Knockout - Post-AMPH 06-10",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# KO - Post-AMPH 16-20
# Variables
genotype <- "KO"
amphetamine <- "POST_16-20"
release <- 4.15
vmax <- 4.8
km <- 32
base_tolerance <- 0.05
plot_duration_sec = 50
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_ko_amph_1620, fil = "Knockout - Post-AMPH 16-20",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
results
# Ad hoc
unique(stim_df$animal)
animal_id <- 1902052
# animal_id <- 1809201
dat_adhoc <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(animal == animal_id & stimulus >= 1 & stimulus <= 3 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_adhoc <- rename(dat_adhoc, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_adhoc$time_sec, dat_adhoc$electrode, geom = "line")
# Constants
pulses <- 30
pulse_freq <- 50
bin_size <- 2.0
electrode_distance <- 1000
dead_space_distance <- 7
diffusion_coefficient <- 2.7 * 10^-6
convert_current <- FALSE
fit_region = "fall"
# Variables
release <- 1.8
vmax <- 4.8
km <- 3
base_tolerance <- 0.05
plot_duration_sec = 10
compare_pulse(dat = dat_adhoc, fil = "Ad Hoc",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# Ad hoc
unique(stim_df$animal)
animal_id <- 1902052
# animal_id <- 1809201
dat_adhoc <- select(stim_df, animal, time_sec, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(animal == animal_id)
qplot(dat_adhoc$time_sec, dat_adhoc$electrode, geom = "line")
pnojai/rwalk documentation built on Nov. 12, 2019, 7:42 a.m.
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library(ggplot2)
library(dplyr)
library(data.table)
# Maha's inputs as of 7/30/2019
# Global variables
pipeline_dir <- "./pipeline"
input_dir <- paste(pipeline_dir, "06_Library", sep = "/")# WT - Pre-AMPH
dat_fil <- "stim_df.csv"
stim_df <- fread(paste(input_dir, dat_fil, sep = "/"))
# WT - Pre-AMPH
dat_merge_wt_pre <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "wt" & stimulus >= 1 & stimulus <= 3 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_wt_pre <- rename(dat_merge_wt_pre, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_wt_pre$time_sec, dat_merge_wt_pre$electrode, geom = "line")
# WT - AMPH_06_10
dat_merge_wt_amph_0610 <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "wt" & stimulus >= 6 & stimulus <= 10 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_wt_amph_0610 <- rename(dat_merge_wt_amph_0610, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_wt_amph_0610$time_sec, dat_merge_wt_amph_0610$electrode, geom = "line")
# WT - AMPH_16_20
dat_merge_wt_amph_1620 <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "wt" & stimulus >= 16 & stimulus <= 20 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_wt_amph_1620 <- rename(dat_merge_wt_amph_1620, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_wt_amph_1620$time_sec, dat_merge_wt_amph_1620$electrode, geom = "line")
# KO - Pre-AMPH
dat_merge_ko_pre <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "ko" & stimulus >= 1 & stimulus <= 3 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_ko_pre <- rename(dat_merge_ko_pre, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_ko_pre$time_sec, dat_merge_ko_pre$electrode, geom = "line")
dat_merge_ko_pre <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "ko" & stimulus >= 1 & stimulus <= 3 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_ko_pre <- rename(dat_merge_ko_pre, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_ko_pre$time_sec, dat_merge_ko_pre$electrode, geom = "line")
# KO - AMPH_06_10
dat_merge_ko_amph_0610 <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "ko" & stimulus >= 6 & stimulus <= 10 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_ko_amph_0610 <- rename(dat_merge_ko_amph_0610, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_ko_amph_0610$time_sec, dat_merge_ko_amph_0610$electrode, geom = "line")
# unique(select(stim_df, animal, genotype, include) %>%
# filter(genotype == "ko" & include == TRUE))
#
# dat_merge_ko_amph_0610 <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
# filter(animal == 1905302 & genotype == "ko" & stimulus >= 8 & stimulus <= 8 & include == TRUE & stim_time_sec <= 120) %>%
# group_by(stim_time_sec) %>%
# summarize(mean(electrode_concentration))
# dat_merge_ko_amph_0610 <- rename(dat_merge_ko_amph_0610, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
# qplot(dat_merge_ko_amph_0610$time_sec, dat_merge_ko_amph_0610$electrode, geom = "line")
# Find the extra peak
# KO - AMPH_16_20
dat_merge_ko_amph_1620 <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(genotype == "wt" & stimulus >= 16 & stimulus <= 20 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_merge_ko_amph_1620 <- rename(dat_merge_ko_amph_1620, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_merge_ko_amph_1620$time_sec, dat_merge_ko_amph_1620$electrode, geom = "line")
# Plot and compile results.
results <- data.frame(genotype = character(),
amphetamine = character(),
release = double(),
vmax = double(),
km = double(),
stringsAsFactors = FALSE)
# Constants
pulses <- 30
pulse_freq <- 50
bin_size <- 2.0
electrode_distance <- 1000
dead_space_distance <- 4
diffusion_coefficient <- 2.7 * 10^-6
convert_current <- FALSE
fit_region = "fall"
# WT - Pre-AMPH
# Maha: 7/30
# Variables
genotype <- "WT"
amphetamine <- "PRE"
release <- 1.8
vmax <- 4.8
km <- 5
base_tolerance <- 0.125
plot_duration_sec = 5
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_wt_pre, fil = "Wild Type - Pre-AMPH",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# WT - Post-AMPH 6-10
# Variables
genotype <- "WT"
amphetamine <- "POST_06-10"
release <- 5.75
vmax <- 4.8
km <- 26
base_tolerance <- 0.5
plot_duration_sec = 25
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_wt_amph_0610, fil = "Wild Type - Post-AMPH 06-10",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# WT - Post-AMPH 16-20
# Variables
genotype <- "WT"
amphetamine <- "POST_16-20"
release <- 4.2
vmax <- 4.8
km <- 32
base_tolerance <- 0.05
plot_duration_sec = 50
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_wt_amph_1620, fil = "Wild Type - Post-AMPH 16-20",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# ----------------- END OF WILD TYPE -----------------#
# ----------------- BEGIN KNOCKOUT -----------------#
# KO - Pre-AMPH
# Variables
genotype <- "KO"
amphetamine <- "PRE"
release <- 1.8
vmax <- 4.8
km <- 5
base_tolerance <- 0.05
plot_duration_sec = 10
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_ko_pre, fil = "Knockout - Pre-AMPH",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# KO - Post-AMPH 6-10
# Variables
genotype <- "KO"
amphetamine <- "POST_06-10"
release <- 4.1
vmax <- 4.8
km <- 26
base_tolerance <- 0.12
plot_duration_sec = 30
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_ko_amph_0610, fil = "Knockout - Post-AMPH 06-10",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# KO - Post-AMPH 16-20
# Variables
genotype <- "KO"
amphetamine <- "POST_16-20"
release <- 4.15
vmax <- 4.8
km <- 32
base_tolerance <- 0.05
plot_duration_sec = 50
if (nrow(results[results$genotype == genotype & results$amphetamine == amphetamine, ]) == 0) {
results[(nrow(results)+1), ] <- c(genotype, amphetamine, release, vmax, km)
} else {
results[results$genotype == genotype &
results$amphetamine == amphetamine, ] <- cbind(genotype, amphetamine, release, vmax, km)
}
compare_pulse(dat = dat_merge_ko_amph_1620, fil = "Knockout - Post-AMPH 16-20",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
results
# Ad hoc
unique(stim_df$animal)
animal_id <- 1902052
# animal_id <- 1809201
dat_adhoc <- select(stim_df, animal, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(animal == animal_id & stimulus >= 1 & stimulus <= 3 & include == TRUE & stim_time_sec <= 120) %>%
group_by(stim_time_sec) %>%
summarize(mean(electrode_concentration))
dat_adhoc <- rename(dat_adhoc, time_sec = stim_time_sec, "electrode" = "mean(electrode_concentration)")
qplot(dat_adhoc$time_sec, dat_adhoc$electrode, geom = "line")
# Constants
pulses <- 30
pulse_freq <- 50
bin_size <- 2.0
electrode_distance <- 1000
dead_space_distance <- 7
diffusion_coefficient <- 2.7 * 10^-6
convert_current <- FALSE
fit_region = "fall"
# Variables
release <- 1.8
vmax <- 4.8
km <- 3
base_tolerance <- 0.05
plot_duration_sec = 10
compare_pulse(dat = dat_adhoc, fil = "Ad Hoc",
vmax = vmax, km = km,
pulses = pulses,
pulse_freq = pulse_freq,
release = release,
bin_size = bin_size,
electrode_distance = electrode_distance,
dead_space_distance = dead_space_distance,
diffusion_coefficient = diffusion_coefficient,
convert_current = convert_current,
fit_region = fit_region,
base_tolerance = base_tolerance,
plot_duration_sec = plot_duration_sec)
# Ad hoc
unique(stim_df$animal)
animal_id <- 1902052
# animal_id <- 1809201
dat_adhoc <- select(stim_df, animal, time_sec, stim_time_sec, electrode_concentration, genotype, stimulus, include) %>%
filter(animal == animal_id)
qplot(dat_adhoc$time_sec, dat_adhoc$electrode, geom = "line")
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