In WendyLiuLab/BiactivationFlow: What the package does (short line)

knitr::opts_chunk$set(echo = FALSE)

library(dplyr)
library(ggplot2)
library(magrittr)

# if(!exists("simultaneous")) devtools::load_all(".")
library(FlowAnalysis)

simultaneous_medians = simultaneous %>% make_medians %>% ungroup
simultaneous_medians_mean = simultaneous_medians %>%
  group_by(antibody, m1_concentration, m2_concentration) %>%
  summarize(mean.CD86=mean(CD86), sd.CD86=sd(CD86),
            mean.CD206=mean(CD206), sd.CD206=sd(CD206),
            n=n()) %>%
  mutate(sem.CD86=sd.CD86/sqrt(n), sem.CD206=sd.CD206/sqrt(n)) %>%
  mutate(ymax.CD86=mean.CD86+sem.CD86, ymin.CD86=mean.CD86-sem.CD86,
         ymax.CD206=mean.CD206+sem.CD206, ymin.CD206=mean.CD206-sem.CD206)

g = ggplot(simultaneous_medians, aes(m1_concentration, CD86, color=antibody)) +
  facet_grid(m2_concentration~Experiment) +
  geom_point() +
  geom_line(aes(group=antibody)) +
  theme_bw()
print(g)

g = ggplot(simultaneous_medians_mean, aes(m1_concentration, mean.CD86, color=antibody)) +
  facet_grid(m2_concentration~.) +
  geom_point() +
  geom_line(aes(group=antibody)) +
  geom_errorbar(aes(ymin=ymin.CD86, ymax=ymax.CD86), width=0.2) +
  theme_bw()
print(g)

g = ggplot(simultaneous_medians, aes(m2_concentration, CD206, color=antibody)) +
  facet_grid(m1_concentration~Experiment) +
  geom_point() +
  geom_line(aes(group=antibody)) +
  theme_bw()
print(g)

g = ggplot(simultaneous_medians_mean, aes(m2_concentration, mean.CD206, color=antibody)) +
  facet_grid(m1_concentration~.) +
  geom_point() +
  geom_line(aes(group=antibody)) +
  geom_errorbar(aes(ymin=ymin.CD206, ymax=ymax.CD206), width=0.2) +
  theme_bw()
print(g)