knitr::opts_chunk$set(echo = TRUE) knitr::opts_chunk$set(message = FALSE) knitr::opts_chunk$set(warning = FALSE) library(ProvidenciaChemo) library(scales)
library(tidyverse) library(scales) metabolites <- read_csv('extdata/Figure_3E_metabolites.csv') library(magrittr) metabolites %<>% pivot_longer(cols = 8:25, names_to = "sample", values_to = "AUC") %>% separate(sample, into = c("genotype", "bacteria", "replicate"), sep = "_") %>% mutate(bacteria = fct_relevel(bacteria, "OP50", "JUb39"), AUC = case_when( AUC == 0 ~ 1, TRUE ~ AUC)) %>% droplevels() Order <- metabolites %>% filter(bacteria == "OP50", genotype == "N2", !is.na(Formula), Formula != "C14H16N2O4") %>% # leave out 5-HT group_by(Formula) %>% summarize(mean = mean(AUC)) %>% arrange(mean) rel_metabolites <- full_join(metabolites, Order) %>% mutate(rel_AUC = AUC/mean) order_rel <- rel_metabolites %>% filter(bacteria == "JUb39", genotype == "N2", !is.na(Formula), Formula != "C14H16N2O4") %>% # leave out 5-HT group_by(Formula) %>% summarize(mean = mean(rel_AUC)) %>% arrange(mean) plot_rel <- rel_metabolites %>% filter(!is.na(Formula), Formula != "C14H16N2O4") %>% mutate(Formula = fct_relevel(Formula, order_rel$Formula)) %>% group_by(bacteria, Formula, genotype) %>% summarise(rel_AUC = mean(rel_AUC)) %>% ggplot(aes(x = bacteria, y = Formula)) + geom_tile(aes(fill = rel_AUC)) + facet_grid(.~genotype) + scale_fill_viridis_c(oob = squish, limits = c(.01,100), trans = "log10", option = "inferno") + theme_minimal() + labs(x = "", y = "Molecular Formula", title = "Relative metabolite abundance", fill = "relative abundance (AUC)") plot_raw <- metabolites %>% filter(!is.na(Formula), Formula != "C14H16N2O4") %>% mutate(Formula = fct_relevel(Formula, Order$Formula)) %>% group_by(bacteria, Formula, genotype) %>% summarise(AUC = mean(AUC)) %>% ggplot(aes(x = bacteria, y = Formula)) + geom_tile(aes(fill = AUC)) + facet_grid(.~genotype) + scale_fill_viridis_c(oob = squish, trans = "log10", limits = c(100000, 10e6), option = "inferno") + theme_minimal() + labs(x = "", y = "Molecular Formula", title = "Metabolite abundance", fill = "Abundance (AUC)") plot_rel
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