In mikeod38/ProvidenciaChemo:

knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(message = FALSE)
knitr::opts_chunk$set(warning = FALSE)
library(ProvidenciaChemo)
library(tidyverse)
library(scales)

metabolites <- read_csv('extdata/Figure_Ext4-6Quant_metabo.csv') %>%
  mutate(bacterial_strain = stringr::str_wrap(bacterial_strain, width = 10),
         bacterial_strain = fct_relevel(bacterial_strain, "OP50", "JUb39"),
         mz604.1689 = case_when(
           is.na(mz604.1689) ~ 0,
           TRUE ~ mz604.1689
         ))

mz499 <- filter(metabolites, sample_type == "worms") %>%
  droplevels()

plot1 <- mz499 %>% ggplot(aes(x = bacterial_strain, y = mz499.1474)) +
  geom_bardots(fillvar = bacterial_strain, dotvar = bacterial_strain) +
  facet_grid(.~worm_genotype) +
  scale_color_plot(palette = "grey-blue-light", drop = TRUE) +
  scale_fill_plot(palette = "grey-blue-light", drop = TRUE) +
  scale_y_continuous(labels = scientific) +
  labs(x = "Bacterial strain",
       y = "Compound m/z 499.1474 \n abundance (AUC)") +
  guides(fill = FALSE,
         color = FALSE)
plot1

lm.499 <- lm(data = mz499, mz499.1474 ~ worm_genotype * bacterial_strain)

lm.499 %>% emmeans::emmeans(pairwise ~ bacterial_strain | worm_genotype) %>% summary()

mz604 <- filter(metabolites, sample_type == "worms") %>%
  droplevels()

plot2 <- mz604 %>% ggplot(aes(x = bacterial_strain, y = mz604.1689)) +
  geom_bardots(fillvar = bacterial_strain, dotvar = bacterial_strain) +
  facet_grid(.~worm_genotype) +
  scale_color_plot(palette = "grey-blue-light", drop = TRUE) +
  scale_fill_plot(palette = "grey-blue-light", drop = TRUE) +
  scale_y_continuous(labels = scientific) +
  labs(x = "Bacterial strain",
       y = "Compound m/z mz604.1689 \n abundance (AUC)") +
  guides(fill = FALSE,
         color = FALSE)
plot2

lm.604 <- lm(data = mz604, mz604.1689 ~ bacterial_strain * worm_genotype)

lm.604 %>% emmeans::emmeans(pairwise ~ bacterial_strain | worm_genotype) %>% summary()

Serotonin <- filter(metabolites, condition == "NGM") %>%
  droplevels()

plot3 <- Serotonin %>% ggplot(aes(x = bacterial_strain, y = `N-Ac_Serotonin`)) +
  geom_bardots(fillvar = bacterial_strain, dotvar = bacterial_strain) +
  facet_grid(~worm_genotype) +
  scale_color_plot(palette = "grey-blue-light", drop = TRUE) +
  scale_fill_plot(palette = "grey-blue-light", drop = TRUE) +
  scale_y_continuous(labels = scientific) +
  labs(x = "Bacterial strain",
       y = "Succinyl-serotonin \n abundance (AUC)") +
  guides(fill = FALSE,
         color = FALSE)

plot3

mikeod38/ProvidenciaChemo documentation built on April 6, 2020, 11:57 p.m.