qPCR

library(tidyverse)

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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## ✔ ggplot2   3.4.1     ✔ tibble    3.1.8
## ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
## ✔ purrr     1.0.1     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
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## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Converted Cq value to aev with: =10^(-(0.3012 * E2) + 11.434)

qpcr <- read.csv("../data/SR-qpcr-data-1.csv", header = TRUE) 

ggplot(data = qpcr, mapping = aes(x = Subgroup, y = CqMean)) + 
  geom_boxplot()  +
  facet_wrap('Target')

## Warning: Removed 1 rows containing non-finite values (`stat_boxplot()`).

ggplot(data = qpcr, mapping = aes(x = Subgroup, y = aev)) + 
  geom_boxplot() +
  facet_wrap('Target')

## Warning: Removed 1 rows containing non-finite values (`stat_boxplot()`).

qpcr %>%
  filter(Target == "Cg_18s(1408/9)") %>%
ggplot(mapping = aes(x = Subgroup, y = aev)) + 
  geom_boxplot()  +
  geom_jitter(aes(color = history), width = 0.1, alpha = 0.7)

qpcr %>%
  filter(Target == "Cg_GAPDH(1172/3)")  %>%
ggplot(mapping = aes(x = Subgroup, y = aev)) + 
  geom_boxplot()  +
  geom_jitter(aes(color = history), width = 0.1, alpha = 0.7)

## Warning: Removed 1 rows containing non-finite values (`stat_boxplot()`).

## Warning: Removed 1 rows containing missing values (`geom_point()`).

qpcr %>%
  filter(Target == "Cg_ATPsynthase(1385/6)")  %>%
ggplot(mapping = aes(x = Subgroup, y = aev)) + 
  geom_boxplot()  +
  geom_jitter(aes(color = history), width = 0.1, alpha = 0.7)

qpcr %>%
  filter(Target == "Cg_citratesynthase(1383/4)")  %>%
ggplot(mapping = aes(x = Subgroup, y = aev)) + 
  geom_boxplot()  +
  geom_jitter(aes(color = history), width = 0.1, alpha = 0.7)