Poly IC qPCR

library(tidyverse)

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr     1.1.2     ✔ readr     2.1.4
## ✔ forcats   1.0.0     ✔ stringr   1.5.0
## ✔ ggplot2   3.4.2     ✔ tibble    3.2.1
## ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
## ✔ purrr     1.0.1     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

qpcr <- read.csv("../data/polyic_pcr.csv", header = TRUE, na.strings = "#VALUE!") 

qpcr <- qpcr %>%
  mutate(treatment = substr(Sample, 1, 1))

ggplot(data = qpcr, mapping = aes(x = treatment, y = ddct)) + 
  geom_boxplot() +
  facet_wrap("Target")

## Warning: Removed 26 rows containing non-finite values (`stat_boxplot()`).

qpcr %>%
  filter(Target == "Cg_cGAS") %>%
ggplot(mapping = aes(x = treatment, y = ddct)) + 
  geom_boxplot() +
  geom_jitter(aes(color = Sample), width = 0.1, alpha = 0.7)

## Warning: Removed 3 rows containing non-finite values (`stat_boxplot()`).

## Warning: Removed 3 rows containing missing values (`geom_point()`).

qpcr %>%
  filter(Target == "Cg_citrate-synt") %>%
ggplot(mapping = aes(x = treatment, y = ddct)) + 
  geom_boxplot() +
  geom_jitter(aes(color = Sample), width = 0.1, alpha = 0.7)

## Warning: Removed 3 rows containing non-finite values (`stat_boxplot()`).

## Warning: Removed 3 rows containing missing values (`geom_point()`).

qpcr %>%
  filter(Target == "Cg_GAPDH") %>%
ggplot(mapping = aes(x = treatment, y = ddct)) + 
  geom_boxplot() +
  geom_jitter(aes(color = Sample), width = 0.1, alpha = 0.7)

## Warning: Removed 2 rows containing non-finite values (`stat_boxplot()`).

## Warning: Removed 2 rows containing missing values (`geom_point()`).

qpcr %>%
  filter(Target == "Cg_IRF2") %>%
ggplot(mapping = aes(x = treatment, y = ddct)) + 
  geom_boxplot() +
  geom_jitter(aes(color = Sample), width = 0.1, alpha = 0.7)

## Warning: Removed 4 rows containing non-finite values (`stat_boxplot()`).

## Warning: Removed 4 rows containing missing values (`geom_point()`).

qpcr %>%
  filter(Target == "Cg_SACSIN") %>%
ggplot(mapping = aes(x = treatment, y = ddct)) + 
  geom_boxplot() +
  geom_jitter(aes(color = Sample), width = 0.1, alpha = 0.7)

## Warning: Removed 7 rows containing non-finite values (`stat_boxplot()`).

## Warning: Removed 7 rows containing missing values (`geom_point()`).

qpcr %>%
  filter(Target == "Cg_VIPERIN") %>%
ggplot(mapping = aes(x = treatment, y = ddct)) + 
  geom_boxplot() +
  geom_jitter(aes(color = Sample), width = 0.1, alpha = 0.7)

## Warning: Removed 3 rows containing non-finite values (`stat_boxplot()`).

## Warning: Removed 3 rows containing missing values (`geom_point()`).