knitr::opts_chunk$set(echo = TRUE) knitr::opts_chunk$set(message = FALSE) knitr::opts_chunk$set(warning = FALSE) library(ProvidenciaChemo) library(tidyverse) library(emmeans) library(modelr) library(tidybayes) library(kableExtra) library(patchwork) theme_set(theme_my)
mcherry<-read_csv(here::here('extdata/Figure_1F_mcherry_oct_correlation.csv')) mcherry <- gather(mcherry, key = location, value = cell_count, ant, mid, post) %>% mutate( cell_count = case_when( cell_count == 0 ~ "none", cell_count == 1 ~ "few (<10)", TRUE ~ "many" )) %>% mutate( cell_count = fct_relevel(cell_count, "none") ) mCherry_JU <- filter(mcherry, condition == "JUb39") mcherry_Post <- filter(mCherry_JU, location == "post") ggplot(filter(mcherry_Post), aes(x=outcome, fill=fct_relevel(cell_count, "none"))) + geom_bar(position='fill') + facet_grid(.~ condition, scales = "free_x") + scale_fill_manual(values=c("#CCCCCC", "#CC6666", "#990000")) + theme_my + guides(fill=guide_legend(title="cell count")) #add n filter(mcherry_Post, condition != 'OP50', location != 'mid') %>% group_by(outcome, location, cell_count) %>% tally() %>% kableExtra::kable() %>% kable_styling(bootstrap_options = c("striped", "hover")) ord.regression.simple <- MASS::polr(filter(mCherry_JU, location == "post"), formula = cell_count ~ outcome ) contrasts.simple <- emmeans::emmeans(ord.regression.simple, pairwise ~ outcome) car::Anova(ord.regression.simple) # for P(Chisq) outcome kable(contrasts.simple$contrasts) %>% kable_styling(bootstrap_options = c("striped", "hover"))
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