In mikeod38/ProvidenciaChemo:

---

title: "Figure_Ext9a_mCherry" author: "Mike O'Donnell" date: "6/12/2019" output: html_document: code_folding: hide

---

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

mcherry <- read_csv(here::here('extdata',"Figure_Ext9a_mCherry.csv")) %>% 
  mutate(
         cell_count = case_when(
           n_cells_code == 0 ~ "none",
           n_cells_code == 1 ~ "few (<10)",
           TRUE ~ "many"
         )) %>% mutate(
           cell_count = fct_relevel(cell_count, "none"),
           food = fct_relevel(food, "OP50", "JUb39"),
           condition = interaction(genotype, food)
         ) %>% droplevels()


plot <- ggplot(mcherry,
       aes(x=food, fill=fct_relevel(cell_count, "none"))) +
  geom_bar(position='fill') +
  facet_grid(.~ genotype, drop = TRUE)  + #, scales = "free_x") +
  scale_fill_manual(values=c("#CCCCCC", "#CC6666", "#990000")) +
  theme_my +
  guides(fill=guide_legend(title="cell count"))


plot

#add n

mcherry %>%
 group_by(genotype, food, cell_count) %>% tally

ord.regression <- MASS::polr(mcherry, formula = cell_count ~ condition)
contrasts <- emmeans::emmeans(ord.regression, pairwise ~ condition)
contrasts$contrasts %>% broom::tidy() %>% mutate(p.adjust = p.adjust(p.value, method = "bonf"))
car::Anova(ord.regression) # for P(Chisq) outcome

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