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Monday, 6 November 2017

Making a chromatography plot with an axis on the right hand side...

While working through our online course, R for Biochemists 101 from the Biochemical Society, Diane Hatziioanou made the following comment:
Could you point me in the direction of help to make a plot with different axes? For example for a character series “fractions” make one plot with two sets of data, one plotted against the right and one against the left y axes where the two y axes could be something like absorbance and activity. Thanks!

This inspired me to create this visualisation:

If you more information, leave a comment below.

Here is the script:
START
#https://stackoverflow.com/questions/43942002/geom-line-with-different-y-axis-scale


library(magrittr)
library(tidyr)

sample_data <- data.frame(fracs = rep(1:20),
  Absorbance = c(0.1, 0.1, 0.1, 0.2, 0.4, 0.1, 0.1, 0.5, 1.0, 0.1,
    0.1, 0.1, 0.5, 0.1, 0.1, 0.2, 0.3, 0.5, 1.0, 0.1),
  Activity = c(32, 33, 35, 150, 287, 39, 35, 40, 42, 32,
    30, 31, 32, 45, 57, 32, 33, 40, 41, 40))

# reformat the data into long format to allow plotting
data <- sample_data %>% gather(y, value, Absorbance:Activity)
data$fracs <- as.integer(data$fracs)

# trial plot for Activity (enzyme activity)
ggplot(data, aes(fracs, value, colour=y)) + 
  geom_line(data=data %>% filter(y=="Activity")) 




# trial plot for Absorbance
ggplot(data, aes(fracs, value, colour=y)) + 
  geom_line(data=data %>% filter(y=="Absorbance"))



# plot the two lines together
ggplot(data, aes(fracs, value, colour=y)) + 
  geom_line(data=data %>% filter(y=="Absorbance")) + 
  geom_line(data=data %>% filter(y=="Activity"))
# but different values makes Absorbance line flat. 





# change the scale for second line
max(sample_data$Absorbance)
max(sample_data$Activity)
scaleby = max(sample_data$Activity)/max(sample_data$Absorbance)

ggplot(data, aes(colour=y)) + 
  geom_line(data=data %>% filter(y=="Activity"),
    aes(x = fracs, y = value)) + 
  geom_line(data=data %>% filter(y=="Absorbance"),
    aes(x = fracs, y=value*scaleby))
# this looks better...


# putting it together with labels etc... 
p <- ggplot() + 
  geom_line(data=data %>% filter(y=="Activity"),
    aes(x = fracs, y = value, colour=y)) + 
  geom_line(data=data %>% filter(y=="Absorbance"),
    aes(x = fracs, y=value*scaleby, colour=y))

# limit for y axis
p <- p + ylim(0,300)

# adding our second scale on the right hand side of the plot
p <- p + scale_y_continuous(sec.axis = sec_axis(~./scaleby, 
    name="Absorbance (570nM)"))
  
# label the x and y axis...
p <- p + ylab("Enzyme activity (units)")
p <- p + xlab("Chromatography fractions")


# This is salt chromatography so adding a line showing 
# the NaCl concentration. 
salt_conc <- data.frame(fracs = rep(1:20),
  conc = c(c(10), seq(from = 10, to = 250, by= 13)))

# salt curve labels
salt_label <- data.frame(x = c(1,20), 
  y = c(10, 250), 
  text = c("[10nM]\nNaCl", "[250nM]\nNaCl"))

# check out the line
ggplot(salt_conc, aes(fracs, conc)) + 
  geom_line() + 
  geom_text(data = salt_label,
    aes(x = x,
      y = y,
      label = text))



# linetype=2 gives a dashed line
p <- p + geom_line(data = salt_conc, aes(fracs, conc),
  linetype = 2)
# add some labels to show the starting and ending concentrations
p <- p + geom_text(data = salt_label,
              aes(x = x,
                y = y,
                label = text),
                size = 2.5)

p <- p + theme_bw()
p <- p + ggtitle("Chromatography plot")
p <- p + theme(legend.position="top", legend.direction="horizontal")
p <- p + theme(legend.title=element_blank())
p





END

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