How to find doubling time of cells with scatterplot in R?

Question

I\'m trying to calculate the doubling time of cells using a scatterplot. This is my dataframe

df = data.frame(\"x\" = 1:5, \"y\" = c(246, 667, 1715, 4867, 11694)         


        

Answer 1

You can visualize the constant rate of change with ggplot2 by scaling the y-axis accordingly:

library(dplyr)
library(ggplot2)
library(broom)
library(scales)

df = data.frame("x" = 1:5, "y" = c(246, 667, 1715, 4867, 11694))

fit <- lm(data = df, log2(y) ~ x)
tidy_fit <- tidy(fit) %>% 
  mutate(x = 3, y = 2048)

ggplot(df, aes(x = x, y = y)) +
  geom_point() +
  scale_y_continuous(name = "log2(y)", 
                     trans = 'log2', 
                     breaks = trans_breaks("log2", function(x) 2^x),
                     labels = trans_format("log2", math_format(2^.x))) +
  geom_smooth(method = "lm", se = FALSE) +
  geom_text(tidy_fit,
            mapping = aes(
              x = x,
              y = y,
              label = paste0("log2(y) = ", round(estimate[1], 2), " + ", round(estimate[2], 2), "x",
                             "\n", "Doubling Time: ", round(1 / tidy_fit$estimate[2], 2), " Days")
            ),
            nudge_x = -1,
            nudge_y = 0.5,
            hjust = 0)

^{Created on 2020-02-03 by the reprex package (v0.3.0)}