Plotting
The loaded spectra can be plotted (with reasonable defaults) in just one line of code:
If plotting multiple samples (as we are here), you can offset the samples in the y axis to be able to more clearly see differences where they may have otherwise overlapped near the baseline:
We can modify this plot a number of ways:
Title & Subtitle
The plot title and subtitle, and the legend title are all
customization. The location of the legend can be changed too! To add a
subtitle, pass a two-element string vector to the
plot_title argument of plot_ftir().
plot_ftir(spectra, plot_title = c("Title of my Spectra Plot", "Plotted with PlotFTIR"), legend_title = "Samples:") |>
move_plot_legend(position = "bottom")
Rename the Plotted Samples
Once a plot has been produced, it’ easy to rename the samples in the
legend. This might be useful when moving from exploratory analysis to a
final output product, or if the sample names in the raw data are very
long and you have short-forms that you want to show on the plot. The
format for the renaming is "new_name" =
"old_name". Not all sample_id need to be
matched, samples without a rename given will retain the name they
currently have.
plot_ftir(spectra) |>
rename_plot_sample_ids(sample_ids = c("Methylbenzene" = "toluene", "C7" = "heptanes"))
Compress Low Energy Region
The lower energy region of a FTIR plot may not be of much interest. We can compress those to both save graphical space and enhance the view of the more complex fingerprint region at higher energy.
You’ll see the usage of
|>- this indicates that the output of this command is being passed to the first argument of the next command. More information on the pipe can be found in the valuable book R for Data Science (2e) by Hadley Wickham, Mine Çetinkaya-Rundel, and Garrett Grolemund. Alternatively you can capture the output of each line of code in a variable and pass that variable on to the next function called.
Limit Wavenumber Range
You can limit wavenumber range (zoom in) to any plot. If we want to look at the OH & CH stretch region, we can limit the spectra to that range.
You might notice the plot itself could be adjusted - a section later
discusses modifications using the ggplot2 functions that
underpin the PlotFTIR package.
Add Markers
We can add markers at any specific wavenumber, to indicate
significant peaks or areas of interest. For example, the 1495 wavenumber
peak corresponds with a carbon-carbon bond (aromatic) vibration. This
marker’s label can be coloured or styled in any way, and the line can be
modified as well. See the ggplot2 documentation for
line_aesthetics and label_aesthetics.
plot_ftir(spectra) |>
add_wavenumber_marker(
wavenumber = 1495,
text = "C-C Aromatic",
line_aesthetics = list("linetype" = "dashed"),
label_aesthetics = list("color" = "#7e0021")
)
Note that any number of markers can be added, before or after other transformations of the spectral plot. The text of multiple markers may overlap.
Putting It All Together
All of the manipulations can be done in sequence to one image. This allows you to easily produce plots modified to your samples and annotated per your need.
plot_ftir(spectra, plot_title = c("My FTIR Plot", "Closeup of Detailed Region 1600 to 800 wavenumbers"), legend_title = "Samples:") |>
move_plot_legend(position = "bottom") |>
zoom_in_on_range(zoom_range = c(1600, 800)) |>
add_wavenumber_marker(wavenumber = 1495, text = "C-C Aromatic", line_aesthetics = c(color = "#7e0021", linetype = "dotted")) |>
add_wavenumber_marker(wavenumber = 817, text = "C-C-O\nsymmetric", line_aesthetics = c(color = "#ff420e", linetype = "dotted")) |>
add_wavenumber_marker(wavenumber = 1380, text = "CH3", line_aesthetics = c(linetype = "dashed")) |>
rename_plot_sample_ids(c("C7 Alkane" = "heptanes", "2-Propanol" = "isopropanol", "Toluene" = "toluene"))
