How can I plot an EC50 value onto my dose-response curve in R?

Question

I used the drm() function in R to find the EC50 value of my data, and then created a dose-response plot. Now have the EC50 value of my data and a plot, but I want to add the EC50 value onto the curve. Is there a way I can do this?

Furthermore, I want to change the scale of the plot. Currently, the plot appears very narrow because of my narrow range of y-values (0 - 0.95). How can I increase the y axis scale?

Here is my dataset-

# A tibble: 6 × 11
    conc    AR1  AR21   AR3  AR22   AR4  AR23    AR5
   <dbl>  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>  <dbl>
1  0     0.943  0.963 0.967 0.947 0.98  0.94  0.96  
2  0.001 0.837  0.743 0.893 0.787 0.983 0.783 0.947 
3  0.01  0.363  0.22  0.857 0.13  0.95  0.107 0.937 
4  0.1   0.0133 0     0     0     0.923 0     0.94  
5  1     0      0     0     0     0.453 0     0.613 
6 10     0      0     0     0     0     0     0.0633

I then fit a four parameter log logistic model

sporecount <- drm(AR1 ~ conc, data = Spore_Count_Averages_Plot_, 
                  fct = LL.4(names = c("Slope", "Lower Limit", "Upper Limit", "ED50"))

Then I plot the model

plot(sporecount, broken = FALSE, xlab="Concentration", ylab="Percent Germinated", lwd=2, 
     cex=1.2, cex.axis=1.2, cex.lab=1.2)

My output is a decent dose response curve, but I want to add the EC50 value onto the graph and increase the y axis scale.

Answer 1

U can adjust accordingly , u can increase y axis by changing ylim = c(0, 1.5)

library(drc)
Spore_Count_Averages_Plot_ <- data.frame(
  conc = c(0, 0.001, 0.01, 0.1, 1, 10),
  AR1 = c(0.943, 0.837, 0.363, 0.0133, 0, 0),
  AR21 = c(0.963, 0.743, 0.22, 0, 0, 0),
  AR3 = c(0.967, 0.893, 0.857, 0, 0, 0),
  AR22 = c(0.947, 0.787, 0.13, 0, 0, 0),
  AR4 = c(0.98, 0.983, 0.95, 0.923, 0.453, 0),
  AR23 = c(0.94, 0.783, 0.107, 0, 0, 0),
  AR5 = c(0.96, 0.947, 0.937, 0.94, 0.613, 0.0633)
)

    # Assuming you have a data frame with your ED50 values
ed_values <- data.frame(concentration = c(0.00672008),
                        estimate = c(0.00672008),
                        std_error = c(0.00052615))

# Plot the model
plot(sporecount, broken = FALSE, xlab = "Concentration", ylab = "Percent Germinated", 
     lwd = 2, cex = 1.2, cex.axis = 1.2, cex.lab = 1.2,
     ylim = c(0, 1))  # Set y-axis limits

# Add vertical line for ED50
abline(v = ed_values$estimate, col = "blue", lty = 2)
text(x = ed_values$estimate + 0.02, y = 0.5,
     labels = paste("ED50 =", round(ed_values$estimate, 3)), col = "blue")

# Add horizontal line at y = 0.5
abline(h = 0.5, col = "green", lty = 2)

text(x = 0.01, y = 0.52, labels = "y = 0.5", col = "green")# u can avoid this things, i included just to show how it works

Note that u can draw both horzontal and vertical line withing single abline function, i just used two time, to make u understand

abline(v = ed_values$estimate, h = 0.5, col = "blue", lty = 2)

If you want to limit the lines to where they meet. To achieve this, you can use segments instead of abline to specify the start and end points of the lines.

# Add lines
segments(y0 = 0.5, x0 = 0.000001, y1 = 0.5, x1 = ed_values$estimate, col = "blue", lty = 2)
segments(x0 = ed_values$estimate, y0 = 0, x1 = ed_values$estimate, 
         y1 = 0.5, col = "blue", lty = 2)

Answer 2

You can get the LD50 value from the drm() by using the ED() command, then simply plot your data (I added confidence interavals too), and you can use the text() command to add anything to a graph you want in base R.

library(drc)

Spore_Count_Averages_Plot_ <- data.frame(
  conc = c(0, 0.001, 0.01, 0.1, 1, 10),
  AR1 = c(0.943, 0.837, 0.363, 0.0133, 0, 0),
  AR21 = c(0.963, 0.743, 0.22, 0, 0, 0),
  AR3 = c(0.967, 0.893, 0.857, 0, 0, 0),
  AR22 = c(0.947, 0.787, 0.13, 0, 0, 0),
  AR4 = c(0.98, 0.983, 0.95, 0.923, 0.453, 0),
  AR23 = c(0.94, 0.783, 0.107, 0, 0, 0),
  AR5 = c(0.96, 0.947, 0.937, 0.94, 0.613, 0.0633)
)

sporecount <- drm(AR1 ~ conc, data = Spore_Count_Averages_Plot_, 
                  fct = LL.4(names = c("Slope", "Lower Limit", "Upper Limit", "ED50")))


plot(sporecount, broken = FALSE, xlab="Concentration", ylab="Percent Germinated", lwd=2, 
     cex=1.2, cex.axis=1.2, cex.lab=1.2, ylim=c(0,1))

#re-run to add confidence interval
plot(sporecount, broken = FALSE, xlab="Concentration", ylab="Percent Germinated", lwd=2, 
     cex=1.2, cex.axis=1.2, cex.lab=1.2, type="confidence", add = T, col="grey")


#get LD50 level
ED(sporecount, c(50), interval="delta")

#add to graph
text(0.1,0.5, "LD50 = 0.00672007", cex=2,font = 2 , col="black")