library(tidyverse)
library(cowplot)
library(broom) 
library(modelr) 
library(viridis)
library(lubridate)
library(hms)
library(knitr)
library(kableExtra)

knitr::opts_chunk$set(tidy.opts=list(width.cutoff=60),tidy=TRUE, echo = TRUE, message=FALSE, warning=FALSE, fig.align="center")

source("../../tools/echem_processing_tools.R")
source("../../tools/plotting_tools.R")

theme_set(theme_1())

Transfer (#2)

SWV

transfer2_data_path = "../data/transfer_2/"
# divide swv into rep and subrep and then subtract 1 from rep
# to match with GC
SWV_transfer2_filenames <- dir(path = transfer2_data_path, pattern = "[swv]+.+[txt]$")

SWV_transfer2_file_paths <- paste(transfer2_data_path, SWV_transfer2_filenames, 
    sep = "")

swv_transfer2_data_cols <- c("E", "i1", "i2")

filename_cols = c("echem", "rep")

swv_skip_rows = 18


swv_transfer2_data <- echem_import_to_df(filenames = SWV_transfer2_filenames, 
    file_paths = SWV_transfer2_file_paths, data_cols = swv_transfer2_data_cols, 
    skip_rows = swv_skip_rows, filename_cols = filename_cols, 
    rep = T, PHZadded = F)

ggplot(swv_transfer2_data, aes(x = E, y = current, color = rep, 
    group = rep)) + geom_path() + facet_wrap(~electrode, scales = "free") + 
    scale_color_viridis() + scale_x_reverse()

swv_transfer2_max <- swv_transfer2_data %>% group_by(rep, electrode) %>% 
    filter(E < -0.15 & E > -0.35) %>% mutate(max_current = max(abs(current))) %>% 
    filter(abs(current) == max_current)


ggplot(swv_transfer2_max, aes(x = minutes, y = max_current, color = electrode)) + 
    geom_point()

ggplot(swv_transfer2_data, aes(x = E, y = current, color = rep, 
    group = rep)) + geom_path() + geom_point(data = swv_transfer2_max, 
    aes(x = E, y = max_current), color = "red", size = 2) + facet_wrap(~electrode, 
    scales = "free") + scale_color_viridis() + scale_x_reverse()

GC

transfer2_data_path = "../data/transfer_2/"
# divide swv into rep and subrep and then subtract 1 from rep
# to match with GC
GC_transfer2_filenames <- dir(path = transfer2_data_path, pattern = "[gc]+.+[txt]$")

GC_transfer2_file_paths <- paste(transfer2_data_path, GC_transfer2_filenames, 
    sep = "")

GC_transfer2_data_cols <- c("E", "i1", "i2")

filename_cols = c("echem", "rep")

GC_skip_rows = 21


GC_transfer2_data <- echem_import_to_df(filenames = GC_transfer2_filenames, 
    file_paths = GC_transfer2_file_paths, data_cols = GC_transfer2_data_cols, 
    skip_rows = GC_skip_rows, filename_cols = filename_cols, 
    rep = T, PHZadded = F)

ggplot(GC_transfer2_data, aes(x = E, y = current, color = rep, 
    group = rep)) + geom_path() + facet_wrap(~electrode, scales = "free") + 
    scale_color_viridis() + scale_x_reverse()

GC_transfer2_max <- GC_transfer2_data %>% group_by(rep, electrode) %>% 
    filter(E < -0.2) %>% mutate(max_current = max(abs(current))) %>% 
    filter(abs(current) == max_current)


ggplot(GC_transfer2_max, aes(x = minutes, y = max_current, color = electrode)) + 
    geom_point()

ggplot(GC_transfer2_data, aes(x = E, y = abs(current), color = rep, 
    group = rep)) + geom_path() + geom_point(data = GC_transfer2_max, 
    aes(x = E, y = max_current), color = "red", size = 2) + facet_wrap(~electrode) + 
    scale_color_viridis() + scale_x_reverse()

SWV vs. GC

tran_max_comb_i1 <- left_join(swv_transfer2_max %>% ungroup() %>% 
    filter(electrode == "i1") %>% mutate(rep = rep - 1), GC_transfer2_max %>% 
    filter(electrode == "i2"), by = c("rep"), suffix = c("_swv", 
    "_gc"))

ggplot(tran_max_comb_i1, aes(x = max_current_swv, y = max_current_gc)) + 
    geom_point() + geom_smooth(data = tran_max_comb_i1 %>% filter(rep < 
    10), method = "lm")

dap_from_swvGC <- function(m, t_p = 1/(2 * 300)) {
    
    psi <- 0.7
    # psi <- 0.75 A <- 0.013 #cm^2
    A <- 0.025  #cm^2
    S <- 18.4  #cm
    d_ap <- (m * A * psi)^2/(S^2 * pi * t_p)
    
    d_ap
}

lm_tran2 <- tidy(lm(max_current_gc ~ max_current_swv, data = tran_max_comb_i1 %>% 
    filter(rep < 10)), conf.int = T) %>% filter(term == "max_current_swv") %>% 
    mutate(dap = dap_from_swvGC(m = estimate)) %>% mutate(dap_high = dap_from_swvGC(m = conf.high)) %>% 
    mutate(dap_low = dap_from_swvGC(m = conf.low)) %>% mutate(dataset = "SWVvsGC")

lm_tran2 %>% kable() %>% kable_styling()

term	estimate	std.error	statistic	p.value	conf.low	conf.high	dap	dap_high	dap_low	dataset
max_current_swv	0.1149031	0.0047281	24.30223	1e-07	0.1037229	0.1260832	2.3e-06	2.7e-06	1.9e-06	SWVvsGC

tran_max_comb_i2 <- left_join(swv_transfer2_max %>% ungroup() %>% 
    filter(electrode == "i2") %>% mutate(rep = rep - 1), GC_transfer2_max %>% 
    filter(electrode == "i2"), by = c("rep"), suffix = c("_swv", 
    "_gc"))

ggplot(tran_max_comb_i2, aes(x = max_current_swv, y = max_current_gc)) + 
    geom_point() + geom_smooth(data = tran_max_comb_i2 %>% filter(rep < 
    10), method = "lm")

lm_tran2_i2 <- tidy(lm(max_current_gc ~ max_current_swv, data = tran_max_comb_i2 %>% 
    filter(rep < 10)), conf.int = T) %>% filter(term == "max_current_swv") %>% 
    mutate(dap = dap_from_swvGC(m = estimate)) %>% mutate(dap_high = dap_from_swvGC(m = conf.high)) %>% 
    mutate(dap_low = dap_from_swvGC(m = conf.low)) %>% mutate(dataset = "SWVvsGC")

lm_tran2_i2 %>% kable() %>% kable_styling()

term	estimate	std.error	statistic	p.value	conf.low	conf.high	dap	dap_high	dap_low	dataset
max_current_swv	0.1556442	0.0034706	44.84624	0	0.1474375	0.1638509	4.2e-06	4.6e-06	3.8e-06	SWVvsGC

Transfer Again (#3)

SWV

transfer3_data_path = "../data/transfer_3/"
# divide swv into rep and subrep and then subtract 1 from rep
# to match with GC
SWV_transfer3_filenames <- dir(path = transfer3_data_path, pattern = "[swv]+.+[txt]$")

SWV_transfer3_file_paths <- paste(transfer3_data_path, SWV_transfer3_filenames, 
    sep = "")

swv_transfer3_data_cols <- c("E", "i1", "i2")

filename_cols = c("echem", "rep")

swv_skip_rows = 18


swv_transfer3_data <- echem_import_to_df(filenames = SWV_transfer3_filenames, 
    file_paths = SWV_transfer3_file_paths, data_cols = swv_transfer3_data_cols, 
    skip_rows = swv_skip_rows, filename_cols = filename_cols, 
    rep = T, PHZadded = F) %>% mutate(minutes = ifelse(minutes < 
    1000, minutes + 1440, minutes))

ggplot(swv_transfer3_data, aes(x = E, y = current, color = rep, 
    group = rep)) + geom_path() + facet_wrap(~electrode, scales = "free") + 
    scale_color_viridis() + scale_x_reverse()

swv_transfer3_max <- swv_transfer3_data %>% group_by(rep, electrode) %>% 
    filter(E < -0.15 & E > -0.35) %>% mutate(max_current = max(abs(current))) %>% 
    filter(abs(current) == max_current)


ggplot(swv_transfer3_max, aes(x = minutes, y = max_current, color = electrode)) + 
    geom_point()

ggplot(swv_transfer3_data, aes(x = E, y = current, color = rep, 
    group = rep)) + geom_path() + geom_point(data = swv_transfer3_max, 
    aes(x = E, y = max_current), color = "red", size = 2) + facet_wrap(~electrode, 
    scales = "free") + scale_color_viridis() + scale_x_reverse()

GC

transfer3_data_path = "../data/transfer_3/"
# divide swv into rep and subrep and then subtract 1 from rep
# to match with GC
GC_transfer3_filenames <- dir(path = transfer3_data_path, pattern = "[gc]+.+[txt]$")

GC_transfer3_file_paths <- paste(transfer3_data_path, GC_transfer3_filenames, 
    sep = "")

GC_transfer3_data_cols <- c("E", "i1", "i2")

filename_cols = c("echem", "rep")

GC_skip_rows = 21


GC_transfer3_data <- echem_import_to_df(filenames = GC_transfer3_filenames, 
    file_paths = GC_transfer3_file_paths, data_cols = GC_transfer3_data_cols, 
    skip_rows = GC_skip_rows, filename_cols = filename_cols, 
    rep = T, PHZadded = F) %>% mutate(minutes = ifelse(minutes < 
    1000, minutes + 1440, minutes))

ggplot(GC_transfer3_data, aes(x = E, y = current, color = rep, 
    group = rep)) + geom_path() + facet_wrap(~electrode, scales = "free") + 
    scale_color_viridis() + scale_x_reverse()

GC_transfer3_max <- GC_transfer3_data %>% group_by(rep, electrode) %>% 
    filter(E < -0.2) %>% mutate(max_current = max(abs(current))) %>% 
    filter(abs(current) == max_current)


ggplot(GC_transfer3_max, aes(x = minutes, y = max_current, color = electrode)) + 
    geom_point()

ggplot(GC_transfer3_data, aes(x = E, y = abs(current), color = rep, 
    group = rep)) + geom_path() + geom_point(data = GC_transfer3_max, 
    aes(x = E, y = max_current), color = "red", size = 2) + facet_wrap(~electrode) + 
    scale_color_viridis() + scale_x_reverse()

SWV vs. GC

tran3_max_comb_i1 <- left_join(swv_transfer3_max %>% ungroup() %>% 
    filter(electrode == "i1") %>% mutate(rep = rep - 1), GC_transfer3_max %>% 
    filter(electrode == "i2"), by = c("rep"), suffix = c("_swv", 
    "_gc"))

ggplot(tran3_max_comb_i1, aes(x = max_current_swv, y = max_current_gc)) + 
    geom_point() + geom_smooth(data = tran3_max_comb_i1 %>% filter(rep < 
    10), method = "lm")

lm_tran3 <- tidy(lm(max_current_gc ~ max_current_swv, data = tran3_max_comb_i1 %>% 
    filter(rep < 10)), conf.int = T) %>% filter(term == "max_current_swv") %>% 
    mutate(dap = dap_from_swvGC(m = estimate)) %>% mutate(dap_high = dap_from_swvGC(m = conf.high)) %>% 
    mutate(dap_low = dap_from_swvGC(m = conf.low)) %>% mutate(dataset = "SWVvsGC")

lm_tran3 %>% kable() %>% kable_styling()

term	estimate	std.error	statistic	p.value	conf.low	conf.high	dap	dap_high	dap_low	dataset
max_current_swv	0.1758578	0.009189	19.13789	3e-07	0.1541293	0.1975863	5.3e-06	6.7e-06	4.1e-06	SWVvsGC

tran3_max_comb_i2 <- left_join(swv_transfer3_max %>% ungroup() %>% 
    filter(electrode == "i2") %>% mutate(rep = rep - 1), GC_transfer3_max %>% 
    filter(electrode == "i2"), by = c("rep"), suffix = c("_swv", 
    "_gc"))

ggplot(tran3_max_comb_i2, aes(x = max_current_swv, y = max_current_gc)) + 
    geom_point() + geom_smooth(data = tran3_max_comb_i2 %>% filter(rep < 
    10), method = "lm")

lm_tran3_i2 <- tidy(lm(max_current_gc ~ max_current_swv, data = tran3_max_comb_i2 %>% 
    filter(rep < 10)), conf.int = T) %>% filter(term == "max_current_swv") %>% 
    mutate(dap = dap_from_swvGC(m = estimate)) %>% mutate(dap_high = dap_from_swvGC(m = conf.high)) %>% 
    mutate(dap_low = dap_from_swvGC(m = conf.low)) %>% mutate(dataset = "SWVvsGC")

lm_tran3_i2 %>% kable() %>% kable_styling()

term	estimate	std.error	statistic	p.value	conf.low	conf.high	dap	dap_high	dap_low	dataset
max_current_swv	0.2152556	0.0058211	36.97831	0	0.2014908	0.2290204	8e-06	9.1e-06	7e-06	SWVvsGC

Soak (#2)

SWV

soak2_data_path = "../data/soak_2/"
# divide swv into rep and subrep and then subtract 1 from rep
# to match with GC
SWV_soak2_filenames <- dir(path = soak2_data_path, pattern = "[swv]+.+[txt]$")

SWV_soak2_file_paths <- paste(soak2_data_path, SWV_soak2_filenames, 
    sep = "")

swv_soak2_data_cols <- c("E", "i1", "i2")

filename_cols = c("echem", "rep")

swv_skip_rows = 18


swv_soak2_data <- echem_import_to_df(filenames = SWV_soak2_filenames, 
    file_paths = SWV_soak2_file_paths, data_cols = swv_soak2_data_cols, 
    skip_rows = swv_skip_rows, filename_cols = filename_cols, 
    rep = T, PHZadded = F)

ggplot(swv_soak2_data, aes(x = E, y = current, color = rep, group = rep)) + 
    geom_path() + facet_wrap(~electrode, scales = "free") + scale_color_viridis() + 
    scale_x_reverse()

swv_soak2_max <- swv_soak2_data %>% group_by(rep, electrode) %>% 
    filter(E < -0.15 & E > -0.35) %>% mutate(max_current = max(abs(current))) %>% 
    filter(abs(current) == max_current)


ggplot(swv_soak2_max, aes(x = minutes, y = max_current, color = electrode)) + 
    geom_point()

ggplot(swv_soak2_data, aes(x = E, y = current, color = rep, group = rep)) + 
    geom_path() + geom_point(data = swv_soak2_max, aes(x = E, 
    y = max_current), color = "red", size = 2) + facet_wrap(~electrode, 
    scales = "free") + scale_color_viridis() + scale_x_reverse()

GC

soak2_data_path = "../data/soak_2/"
# divide swv into rep and subrep and then subtract 1 from rep
# to match with GC
GC_soak2_filenames <- dir(path = soak2_data_path, pattern = "[gc]+.+[txt]$")

GC_soak2_file_paths <- paste(soak2_data_path, GC_soak2_filenames, 
    sep = "")

GC_soak2_data_cols <- c("E", "i1", "i2")

filename_cols = c("echem", "rep")

GC_skip_rows = 21


GC_soak2_data <- echem_import_to_df(filenames = GC_soak2_filenames, 
    file_paths = GC_soak2_file_paths, data_cols = GC_soak2_data_cols, 
    skip_rows = GC_skip_rows, filename_cols = filename_cols, 
    rep = T, PHZadded = F)

ggplot(GC_soak2_data, aes(x = E, y = current, color = rep, group = rep)) + 
    geom_path() + facet_wrap(~electrode, scales = "free") + scale_color_viridis() + 
    scale_x_reverse()

GC_soak2_max <- GC_soak2_data %>% group_by(rep, electrode) %>% 
    filter(E < -0.2) %>% mutate(max_current = max(abs(current))) %>% 
    filter(abs(current) == max_current)


ggplot(GC_soak2_max, aes(x = minutes, y = max_current, color = electrode)) + 
    geom_point()

ggplot(GC_soak2_data, aes(x = E, y = abs(current), color = rep, 
    group = rep)) + geom_path() + geom_point(data = GC_soak2_max, 
    aes(x = E, y = max_current), color = "red", size = 2) + facet_wrap(~electrode) + 
    scale_color_viridis() + scale_x_reverse()

SWV vs. GC

soak_max_comb_i1 <- left_join(swv_soak2_max %>% ungroup() %>% 
    filter(electrode == "i1") %>% mutate(rep = rep - 1), GC_soak2_max %>% 
    filter(electrode == "i2"), by = c("rep"), suffix = c("_swv", 
    "_gc"))

ggplot(soak_max_comb_i1, aes(x = max_current_swv, y = max_current_gc)) + 
    geom_point() + geom_smooth(data = soak_max_comb_i1, method = "lm")

lm_soak2 <- tidy(lm(max_current_gc ~ max_current_swv, data = soak_max_comb_i1 %>% 
    filter(rep < 10)), conf.int = T) %>% filter(term == "max_current_swv") %>% 
    mutate(dap = dap_from_swvGC(m = estimate)) %>% mutate(dap_high = dap_from_swvGC(m = conf.high)) %>% 
    mutate(dap_low = dap_from_swvGC(m = conf.low)) %>% mutate(dataset = "SWVvsGC")

lm_soak2 %>% kable() %>% kable_styling()

term	estimate	std.error	statistic	p.value	conf.low	conf.high	dap	dap_high	dap_low	dataset
max_current_swv	0.1376003	0.0022443	61.31038	0	0.1322933	0.1429073	3.3e-06	3.5e-06	3e-06	SWVvsGC

soak_max_comb_i2 <- left_join(swv_soak2_max %>% ungroup() %>% 
    filter(electrode == "i2") %>% mutate(rep = rep - 1), GC_soak2_max %>% 
    filter(electrode == "i2"), by = c("rep"), suffix = c("_swv", 
    "_gc"))

ggplot(soak_max_comb_i2, aes(x = max_current_swv, y = max_current_gc)) + 
    geom_point() + geom_smooth(data = soak_max_comb_i2, method = "lm")

lm_soak2_i2 <- tidy(lm(max_current_gc ~ max_current_swv, data = soak_max_comb_i2 %>% 
    filter(rep < 10)), conf.int = T) %>% filter(term == "max_current_swv") %>% 
    mutate(dap = dap_from_swvGC(m = estimate)) %>% mutate(dap_high = dap_from_swvGC(m = conf.high)) %>% 
    mutate(dap_low = dap_from_swvGC(m = conf.low)) %>% mutate(dataset = "SWVvsGC")

lm_soak2_i2 %>% kable() %>% kable_styling()

term	estimate	std.error	statistic	p.value	conf.low	conf.high	dap	dap_high	dap_low	dataset
max_current_swv	0.1973125	0.0032121	61.42831	0	0.1897171	0.2049078	6.7e-06	7.3e-06	6.2e-06	SWVvsGC

Output files

# SWV
swv_max_ctDNA <- bind_rows(swv_transfer2_max %>% mutate(reactor = "transfer_2"), 
    swv_transfer3_max %>% mutate(reactor = "transfer_3"), swv_soak2_max %>% 
        mutate(reactor = "soak_2"))

# write_csv(swv_max_ctDNA,
# '08_13_19_processed_swv_max_ctDNA.csv')

# GC
gc_max_ctDNA <- bind_rows(GC_transfer2_max %>% mutate(reactor = "transfer_2"), 
    GC_transfer3_max %>% mutate(reactor = "transfer_3"), GC_soak2_max %>% 
        mutate(reactor = "soak_2"))

# write_csv(gc_max_ctDNA,
# '08_13_19_processed_gc_max_ctDNA.csv')

# SWV - GC
swvGC_ctDNA <- bind_rows(tran_max_comb_i1 %>% mutate(reactor = "transfer_2"), 
    tran_max_comb_i2 %>% mutate(reactor = "transfer_2"), tran3_max_comb_i1 %>% 
        mutate(reactor = "transfer_3"), tran3_max_comb_i2 %>% 
        mutate(reactor = "transfer_3"), soak_max_comb_i1 %>% 
        mutate(reactor = "soak_2"), soak_max_comb_i2 %>% mutate(reactor = "soak_2"))

# write_csv(swvGC_ctDNA,
# '08_13_19_processed_swvGC_ctDNA.csv')

Agarose ctDNA

Scott Saunders

08_13_19

Transfer (#2)

SWV

GC

SWV vs. GC

Transfer Again (#3)

SWV

GC

SWV vs. GC

Soak (#2)

SWV

GC

SWV vs. GC

Output files