knitr::opts_chunk$set(echo = TRUE) knitr::opts_chunk$set(message = FALSE) knitr::opts_chunk$set(warning = FALSE) devtools::install_github("https://github.com/SenguptaLab/ProvidenciaChemo.git") library(ProvidenciaChemo)
library(tidyverse) library(emmeans) library(modelr) library(tidybayes) library(kableExtra) filepath <- here::here("extdata/Figure_3C_SOSJUKO.csv") SOSKO <- read_csv(filepath) %>% mutate(food = fct_relevel(food, c("OP50", "JUb39", "JUb39; tdcDel::cmR", "JUb39; delAADC"))) lmer <- SOSKO %>% lme4::lmer(., formula = log10(response.time) ~ food + (1|date) + (1|plateID)) library(rstanarm) stan_glm <- SOSKO %>% rstanarm::stan_lmer(., formula = log(response.time) ~ food + (1 | date) + (1|plateID), cores = 4, chains = 4, seed = 637, adapt_delta = 0.99) # get Bayesian cred intervals for differences between food fitted1 <- emmeans::ref_grid(stan_glm) %>% emmeans::contrast("trt.vs.ctrl") %>% coda::as.mcmc() %>% bayesplot::mcmc_intervals_data(prob = 0.66, prob_outer = 0.95) %>% mutate(data_type = "fit", food = c("JUb39", "JUb39; tdcDel::cmR", "JUb39; delAADC", "JUb39; tdcDel::cmR delAADC")) %>% mutate(food = factor(food, levels = c("OP50", "JUb39", "JUb39; tdcDel::cmR", "JUb39; delAADC", "JUb39; tdcDel::cmR delAADC"))) #%>% #mutate_if(is.numeric, function(.) {. * -1}) plot <- format_SOS(SOSKO, day_correct = genotype) %>% ggplot(aes(x = data_type)) + geom_relLatency(fitted = fitted1, fillvar = food, dotvar = food, yvar = rel_log) + scale_color_plot("grey-blue-light", drop = TRUE) + scale_fill_plot("grey-blue-light", drop = TRUE) + facet_grid(.~genotype+food) + add.n('data_type', y.pos = -1.6) + labs(x = "genotype", y = "relative reversal latency [log(s)]") + guides(colour = FALSE, fill = FALSE) + coord_cartesian(ylim = c(-1.7,2)) + theme(axis.text.x = element_blank()) plot lmer %>% emmeans::ref_grid() %>% emmeans::contrast(method = "pairwise", type = "response") %>% broom::tidy() %>% mutate_if(is.numeric, ~ round(., 3)) %>% kable() %>% kable_styling(bootstrap_options = c("striped", "hover"))
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