Tuesday 16 June 2015

Drawing the protein assay with ggplot

I have been persuaded by Steph Locke during todays meeting of the Cardiff R Users Group that I should use ggplot for all the plots during our R for Biochemist Training Day. For that reason, I have written the script below which uses ggplot to graph the protein assay:

# START of SCRIPT
library(ggplot2)

# Protein Concentrations
prot <- c(0.000, 0.016, 0.031, 0.063, 0.125, 0.250, 0.500, 1.000, 
          0.000, 0.016, 0.031, 0.063, 0.125, 0.250, 0.500, 1.000) 

# Absorbance from my protein assay
abs <- c(0.329, 0.352, 0.349, 0.379, 0.417, 0.491, 0.668, 0.956, 
         0.327, 0.341, 0.355, 0.383, 0.417, 0.446, 0.655, 0.905)

# Convert into data.frame to plot with ggplot
data <- as.data.frame(prot)
data$abs <- abs

#Calculate the line using the linear model function
line <- lm(abs~prot)

#Equation of a line y = mx + c
#In our case abs = slope * prot + intercept
# ukn.prot = (abs - intercept)/slope
int <- summary(line)$coefficients[1]
slope <- summary(line)$coefficients[2]

#now calculate some unknown protein concs from absorbances
#put the unknowns into a vector
abs.ukns <- c(0.554, 0.568, 0.705)

#rearrange the equation of the line to ukn.prot = (abs - intercept)/slope
prot.ukns <- (abs.ukns - int)/slope

# create the object with the graph in it. 
p <- ggplot(data=data,          # specify the data frame with data
        aes(x=prot, y=abs)) +   # specify the x and y for the graph
        geom_point() +          # make a scatter plot
        stat_smooth(method = "lm") +  # add a linear model line
        xlab("[Protein] (microg/ml)") +   # label x-axis
        ylab("Absorbance (570nm)") +    # label y-axis
        ggtitle("Protein Assay 20th April 2015") +  # add a title
        theme_bw() +      # a simple theme
        expand_limits(y=c(0.25,1)) +    # customise the y-axis
        annotate(geom="text", x=0.85, y= 0.6, label="Abs         Prot",  color="red")

#put the answers on the graph
for (i in 1:length(abs.ukns)){
  p <- p + annotate(geom="text", x = 0.8, y = (0.6 - i/20), label=abs.ukns[i])
  p <- p + annotate(geom="text", x = 0.92, y = (0.6 - i/20), label=round(prot.ukns[i], 3))
}

p # show us the graph...

# END OF SCRIPT

1 comment:

  1. I’m really amazed with your posting skills as well as with the layout on your blog site. Very informative and well written post! Quite interesting and nice topic chosen for the post Nice Post keep it up.Excellent post.
    example of assay

    ReplyDelete

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