ggplotting some qPCR – Tumbling Oysters

Code

library(tidyverse)

── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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✔ 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)

Code

qpcr <- read.csv("https://raw.githubusercontent.com/sr320/lsamp-2023/main/data/SR-qpcr-data-1.csv", header = TRUE)

Code

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

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

Code

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

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

Code

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)

Code

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()`).

Code

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)

Code

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)

Citation

BibTeX citation:

@online{roberts2023,
  author = {Roberts, Steven},
  title = {Ggplotting Some {qPCR}},
  date = {2023-07-21},
  url = {https://sr320.github.io/tumbling-oysters/posts/sr320-02-qpcr/},
  langid = {en}
}

For attribution, please cite this work as:

Roberts, Steven. 2023. “Ggplotting Some qPCR.” July 21, 2023. https://sr320.github.io/tumbling-oysters/posts/sr320-02-qpcr/.