knitr::opts_chunk$set(echo = TRUE) knitr::opts_chunk$set(message = FALSE) knitr::opts_chunk$set(warning = FALSE) library(ProvidenciaChemo)
library(tidyverse) library(patchwork) library(tidybayes) library(modelr) library(emmeans) library(magrittr) library(emmeans) filepath <- here::here("extdata/Figure_1B_PYb007.csv") MOb_data <- read.csv(filepath) %>% dplyr::filter(date != "5_12_17") %>% format_AvoidData(day.correct = "OP50") %>% mutate(plate = factor(seq(1:nrow(.)))) %>% droplevels() glmm <- lme4::glmer(data = MOb_data, formula = cbind(nCue,nControl) ~ strain + (1|date) + (1|plate), family = binomial) stan_glmm <- rstanarm::stan_glmer(data = MOb_data, formula = cbind(nCue,nControl) ~ strain + (1|date) + (1|plate), chains = 4, cores = 4, seed = 2000, iter=6000, family = binomial, control = list(adapt_delta=0.99)) fitted <- recenter_fittedValues(MOb_data, stan_glmm, day.correct = "OP50", BayesFit = "HDI") MOb_plot <- MOb_data %>% plot_plasticityIndex(xvar = strain, plotColors = "grey-blue", BayesFit = TRUE, width = 0.2, alpha = 0.7, bar = TRUE, n_pos = -2) + labs(title = "1-oct (corrected)") + scale_color_plot(palette = "2-Ps", drop = TRUE) + scale_fill_plot(palette = "2-Ps", drop = TRUE) + guides(color = FALSE) + labs(fill="strain") + facet_grid(~strain) + coord_cartesian(ylim = c(-2.5, 3.25)) + figure.axes() #glm.contrasts <- emmeans::emmeans(glmm, pairwise ~ strain | treatment) glm.contrasts.1 <- emmeans::ref_grid(glmm) %>% emmeans::contrast(., method = "pairwise") %>% broom::tidy() %>% filter(level1 == "OP50") %>% mutate(strain = forcats::as_factor(c("JUb39", "MOb007")), data_type = forcats::as_factor(rep("raw", 2))) MOb_plot + geom_text(data = glm.contrasts.1, aes(label = paste0("P~",round(p.value, 3)), y = max(1.3*MOb_data$rel.Logit)))
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