Capsaicinoids Chromatograms

library(rstatix)
library(tidyverse)

Extract standard data set

dataset = read_delim('std_signals.csv', delim =",")

Rows: 3001 Columns: 26── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
dbl (26): TIME, 1000CAPT1, 1000CAPT2, 1000CAPT3, 1000DHCT1, 1000DHCT2, 1000DHCT3, 500MIX, 250MIXT1, 250MIXT2, 250MIXT3...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

dataset_new = read_delim('calibration_and_pepper_signals.csv', delim=',')

Rows: 3000 Columns: 33── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
dbl (33): Time, mix_2_5_1, mix_2_5_2, mix_2_5_3, mix_10_1, mix_10_2, mix_10_3, mix_20_1, mix_20_2, mix_20_3, mix_40_1,...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

CAP_1000 = dataset %>% 
  select(1:4)

DHC_1000 = dataset %>% 
  select(1, 5, 6, 7)

MIX_500 = dataset %>% 
  select(1, 8)

MIX_250 = dataset %>% 
  select(1, 9:11)

MIX_100 = dataset %>% 
  select(1, 12:14)

MIX_80 = dataset %>% 
  select(1, 15:17)

MIX_50 = dataset %>% 
  select(1, 18:20)

MIX_20 = dataset %>% 
  select(1, 21:23)

MIX_10 = dataset %>% 
  select(1, 24:26)

colnames(CAP_1000) = colnames(DHC_1000 )= colnames(MIX_500 ) = colnames(MIX_250) = colnames(MIX_100 ) = colnames(MIX_80 ) =
  colnames(MIX_50 ) = colnames(MIX_20 ) = colnames(MIX_10) = c("time", "trial_1", "trial_2", "trial_3")

CAP_1000_LONG = CAP_1000 %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

DHC_1000_LONG = DHC_1000 %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

#MIX_500_LONG = MIX_500 %>% 
#  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
#               names_to = "trial",
#               values_to = "area")

MIX_250_LONG = MIX_250 %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

MIX_100_LONG = MIX_100 %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

MIX_80_LONG = MIX_80 %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

MIX_50_LONG = MIX_50 %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

MIX_20_LONG = MIX_50 %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

MIX_10_LONG = MIX_50 %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

mix_2_5_new = dataset_new %>% 
  select(1:4)

mix_10_new = dataset_new %>% 
  select(1, 5:7)

mix_20_new = dataset_new %>% 
  select(1, 8:10)

mix_40_new = dataset_new %>% 
  select(1, 11:12)

mix_60_new = dataset_new %>% 
  select(1, 13:15)

mix_80_new = dataset_new %>% 
  select(1, 16:18)

mix_100_new = dataset_new %>% 
  select(1, 19:21)

xiao_flesh_new = dataset_new %>% 
  select(1, 22:24)

xiao_5050_new = dataset_new %>% 
  select(1, 25:27)

xiao_100_new = dataset_new %>% 
  select(1, 28:30)

gbp_flesh_new = dataset_new %>% 
  select(1, 31:33)

colnames(mix_2_5_new) = colnames(mix_10_new )= colnames(mix_20_new) = colnames(mix_40_new) = colnames(mix_60_new ) = colnames(mix_80_new ) =
  colnames(mix_100_new ) = colnames(xiao_flesh_new ) = colnames(xiao_5050_new) = colnames(xiao_100_new) = colnames(gbp_flesh_new) = c("time", "trial_1", "trial_2", "trial_3")

mix_2_5_new_long = mix_2_5_new %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

mix_10_new_long = mix_10_new %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

mix_20_new_long = mix_20_new %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

mix_40_new_long = mix_40_new %>% 
  pivot_longer(cols = c( "trial_1", "trial_2"),
               names_to = "trial",
               values_to = "area")

mix_60_new_long = mix_60_new %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

mix_80_new_long = mix_80_new %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

mix_100_new_long = mix_100_new %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

xiao_flesh_new_long = xiao_flesh_new %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

xiao_5050_new_long = xiao_5050_new %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

xiao_100_new_long = xiao_100_new %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

gbp_flesh_new_long = gbp_flesh_new %>% 
  pivot_longer(cols = c( "trial_1", "trial_2", "trial_3"),
               names_to = "trial",
               values_to = "area")

capsaicin_1000_chromatogram = ggplot(data=CAP_1000_LONG, mapping = aes(x= time, y=area, color = trial)) +
  geom_line() +
  ggtitle(expression("Chromatogram of Capsaicin (1000"*mu*"g/mL)")) +
  theme(plot.title = element_text(face = 'bold', size = 20, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.3) +
  labs(x="Time (min)", y="Area", color="Trial")

ggplot(data=DHC_1000_LONG, mapping = aes(x= time, y=area, color = trial)) +
  geom_line() +
  ggtitle(expression("Chromatogram of Dihydrocapsaicin (1000"*mu*"g/mL)")) +
  theme(plot.title = element_text(face = 'bold', size = 16, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.3) +
  labs(x="Time (min)", y="Area", color="Trial")

ggplot(data=MIX_250_LONG, mapping = aes(x= time, y=area, color = trial)) +
  geom_line() +
  ggtitle(expression("Chromatogram of Capsaicin & Dihydrocapsaicin (250"*mu*"g/mL)")) +
  theme(plot.title = element_text(face = 'bold', size = 16, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.3) +
  labs(x="Time (min)", y="Area", color="Trial")

ggplot(data=MIX_100_LONG, mapping = aes(x= time, y=area, color = trial)) +
  geom_line() +
  ggtitle(expression("Chromatogram of Capsaicin & Dihydrocapsaicin (100"*mu*"g/mL)")) +
  theme(plot.title = element_text(face = 'bold', size = 16, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.3) +
  labs(x="Time (min)", y="Area", color="Trial")

ggplot(data=MIX_80_LONG, mapping = aes(x= time, y=area, color = trial)) +
  geom_line() +
  ggtitle(expression("Chromatogram of Capsaicin & Dihydrocapsaicin (80"*mu*"g/mL)")) +
  theme(plot.title = element_text(face = 'bold', size = 16, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.3) +
  labs(x="Time (min)", y="Area", color="Trial")

ggplot(data=MIX_50_LONG, mapping = aes(x= time, y=area, color = trial)) +
  geom_line() +
  ggtitle(expression("Chromatogram of Capsaicin & Dihydrocapsaicin (50"*mu*"g/mL)")) +
  theme(plot.title = element_text(face = 'bold', size = 16, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.3) +
  labs(x="Time (min)", y="Area", color="Trial")

ggplot(data=MIX_20_LONG, mapping = aes(x= time, y=area, color = trial)) +
  geom_line() +
  ggtitle(expression("Chromatogram of Capsaicin & Dihydrocapsaicin (20"*mu*"g/mL)")) +
  theme(plot.title = element_text(face = 'bold', size = 16, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.3) +
  labs(x="Time (min)", y="Area", color="Trial")

ggplot(data=MIX_10_LONG, mapping = aes(x= time, y=area, color = trial)) +
  geom_line() +
  ggtitle(expression("Chromatogram of Capsaicin & Dihydrocapsaicin (10"*mu*"g/mL)")) +
  theme(plot.title = element_text(face = 'bold', size = 16, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.3) +
  labs(x="Time (min)", y="Area", color="Trial")

gbp_vs_xiao = dataset_new %>% 
  select(1, 22, 31)

colnames(gbp_flesh_new) = c("Time", "Xiao", "Green_Bell")

gbp_vs_xiao_long = gbp_vs_xiao %>% 
  pivot_longer(cols = -c("Time"),
               names_to = "Pepper",
               values_to = "area")

ggplot(data=gbp_vs_xiao_long, mapping = aes(x= Time, y= area, color = Pepper)) +
  geom_line(mapping = aes(x= Time, y=area)) +
  ggtitle("Xiao vs Green Bell Pepper Chromatogram") +
  theme(plot.title = element_text(face = 'bold', size = 16, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.8) +
  labs(x="Time (min)", y="Area", color="Pepper")

ggsave(filename = "Xiao_vs_gbp.png")

Saving 7.29 x 4.5 in image

gbp_vs_xiao_long_filter = gbp_vs_xiao_long %>% 
  filter(Time > 5)

ggplot(data=gbp_vs_xiao_long_filter, mapping = aes(x= Time, y= area, color = Pepper)) +
  geom_line(mapping = aes(x= Time, y=area)) +
  ggtitle("Xiao vs Green Bell Pepper Chromatogram (Zoomed)") +
  theme(plot.title = element_text(face = 'bold', size = 16, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.8) +
  labs(x="Time (min)", y="Area", color="Pepper")

ggsave(filename = "Xiao_vs_gbp_zoomed.png")

Saving 7.29 x 4.5 in image

ggplot(data=mix_100_new, mapping = aes(x= time, y=trial_1)) +
  geom_line() +
  ggtitle(expression("Chromatogram of Capsaicin and Dihydrocapsaicin Mixture at (100 "*mu*"g/mL)")) +
  theme(plot.title = element_text(face = 'bold', size = 14, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.3) +
  labs(x="Retention Time (min)", y="Absorbance (mAU)") +
  annotate("text", x= 10, y=90, label="Capsaicin") +
  annotate("text", x= 16.2, y=90, label="Dihydrocapsaicin")

ggplot(data=xiao_100_new, mapping = aes(x= time, y=trial_1)) +
  geom_line() +
  ggtitle("Xiao Extracted in 100% MeCN") +
  theme(plot.title = element_text(face = 'bold', size = 14, hjust = 0.5), 
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.3) +
  labs(x="Retention Time (min)", y="Absorbance (mAU)") 

mix_100 = MIX_100[-3001,]
colnames(mix_100) = c("og_time", "og_trial_1", "og_trial_2", "og_trial_2")
colnames(mix_100_new) = c("new_time", "new_trial_1", "new_trial_2", "new_trial_3")
mix_shift = cbind(mix_100, mix_100_new)
mix_shift_long = pivot_longer(data = mix_shift,
                              cols = starts_with("og_trial") | starts_with("new_trial"),
                              names_to = "trial_age",
                              values_to = "area")
mix_shift_long = mix_shift_long %>% mutate(time = rowMeans(cbind(og_time, new_time)))

ggplot(data=mix_shift_long, mapping = aes(x= time, y= area, color = trial_age)) +
  geom_line(mapping = aes(x= time, y=area)) +
  ggtitle("Chromatogram Shift in Mix") +
  theme(plot.title = element_text(face = 'bold', size = 16, hjust = 0.5),
        axis.title = element_text(face='bold'), panel.background = element_rect('azure2'),
        aspect.ratio = 0.8) +
  labs(x="Time (min)", y="Area", color="Trial and Age")