In vanNimwegenLab/vngMoM: vngMoM

Plot a few random single-cell traces

myframes %>% 
  filter(time_start > 0, !end_type %in% "exit") %>% 
  group_by(condition, cell) %>% nest() %>% 
  group_by(condition) %>% sample_n(10L) %>% 
  unnest() %>% ungroup() %>% 
  ggplot(aes(time_sec, length_um, group=cell)) +
  facet_wrap(~condition, ncol=1) +
  geom_line() +
  scale_y_continuous(trans="log2") +
  NULL

mycells <-
  myframes %>% 
  group_by(condition, antibio, date, pos, gl, id) %>% 
  filter(time_sec < 6 * 3600) %>% 
  filter(time_start > 0, n() > 3) %>% 
  # filter(date == "20200922", pos == 22, gl == 19, id == 48) %>% 
  # select(time_sec, length_um)
  nest() %>% 
  mutate(
    n=map_dbl(data, nrow),
    end_type=map_chr(data, ~unique(.$end_type)),
    mod=map(data, ~lm(log(length_um)~time_sec, data=.))
  )


mycells %>% 
  # filter(n > 10) %>% 
  filter(end_type=="div") %>%
  mutate(
    grate=map_dbl(mod, ~coef(.)[2]),
    grate_se=map_dbl(mod, ~summary(.)$coefficients[2,2]),
    r2=map_dbl(mod, ~summary(.)$r.squared),
  ) %>% 
  ggplot(aes(grate/log(2) * 3600)) +
  stat_ecdf(aes(col=antibio, group=interaction(date, antibio))) +
  coord_cartesian(xlim=c(0, 2)) +
  labs(x="growth rate (dbl/h)", y="cumulative probability") +
  NULL

mycells %>% 
  filter(end_type=="div") %>% 
  mutate(
    grate=map_dbl(mod, ~coef(.)[2]),
    grate_se=map_dbl(mod, ~summary(.)$coefficients[2,2]),
    r2=map_dbl(mod, ~summary(.)$r.squared),
  ) %>% 
  ggplot(aes(grate/log(2) * 3600)) +
  stat_ecdf(aes(col=date, group=interaction(date, antibio))) +
  coord_cartesian(xlim=c(0, 2)) +
  labs(x="growth rate (dbl/h)", y="cumulative probability") +
  NULL

mycells %>% 
  # filter(n > 10) %>% 
  filter(end_type=="div") %>%
  mutate(
    r2=map_dbl(mod, ~summary(.)$r.squared),
  ) %>% 
  ggplot(aes(r2)) +
  stat_ecdf(aes(col=date, group=interaction(date, antibio))) +
  coord_cartesian(xlim=c(0.9, 1)) +
  labs(x="Pearson correlation r2", y="cumulative probability") +
  NULL

mycells %>% 
  # filter(n > 10) %>% 
  filter(end_type=="div") %>%
  ggplot(aes(n)) +
  stat_ecdf(aes(col=date, group=interaction(date, antibio))) +
  labs(y="cumulative probability") +
  NULL