Making a box and whisker plot with some published proteomic data...

Updated: 1st July 2019 - the source file has changed so some of the script had to be changed.
I'm preparing some teaching materials for another Biochemical Society R training event with the draft title of R for Biochemists 201. Some more advanced material based on feedback for participants of R for Biochemists 101.
In preparation, I've been looking at published proteomics data. I've come across a nice paper by a group in the Barts Cancer Institute in London. The paper is entitled "Proteomic and genomic integration identifies kinase and differentiation determinants of kinase inhibitor sensitivity in leukemia cells". It was published in the journal Leukaemia.
I visited their lab once many years ago and I have heard the senior author, Pedro Cutillas, talk.  It is very interesting work, I think.
They have made their data available so I've spend some time writing a script that makes one part of Figure 1a - a nice box and whisker plot.

Here is the plot:

and here is the script:
START
## data import
library(readxl)
library(ggplot2)
link <- "https://static-content.springer.com/esm/art%3A10.1038%2Fs41375-018-0032-1/MediaObjects/41375_2018_32_MOESM2_ESM.xlsx"
download.file(link, "temp_data")
data <- read_excel("temp_data", skip=2) 
# skip = 2 stops the first two rows being part of the file
# the next row is used as titles of the columns
# skip needs to be determined by looking at the data

# remove bottom two rows as only 36 patients
data <- data[1:36,]


# using the geom_boxplot() function, we can draw our graph
ggplot(data = data,
    aes(FAB, log10(`MEKi (trametinib)...13`), colour = FAB)) +
    geom_boxplot(na.rm = TRUE)

# we can make it look a bit more like the plot in the paper using geom_jitter()
plot <- ggplot(data = data,
    aes(FAB, log10(`MEKi (trametinib)...13`), colour = FAB)) +
    geom_boxplot(na.rm = TRUE) +
    geom_jitter(width=0.15, na.rm = TRUE) +
    theme_bw() +
    labs( y = "Log10(EC50)nM",
        title = "Sensitivity of AML patients samples to MEK inhibitor", 
        subtitle = "Casado et al (2018) Leukaemia 32:1818–1822
doi:10.1038/s41375-018-0032-1") +
    theme(legend.position="none")
plot

# to print a high resolution of this the tiff() function can be used. 
tiff("plot.tiff", height = 12, width = 17, units = 'cm', compression = "lzw", res = 300)
plot
dev.off()
END


Some resources:

• Link to the published article: Casado et al (2018) Leukemiavolume 32, pages1818–1822 
• Reference page for geom_boxplot()
• Reference page for geom_jitter()
• This plot is about kinases so you might like to draw the kinome in R
• Plotting high resolution plots in R