Tutorial 3: Customising 1D plots

Here, we will learn how to change various aspects of the basic 1D plot. We will continue using the data_1d object that we imported in Tutorial 1: Reading data.

Recall that plotting consists of three parts: staging, construction, and display. In this tutorial, we will only cover options that pertain to staging: that is, options that only affect individual spectra. In the next tutorial, when we discuss how to plot multiple spectra on the same axes, we will discuss the various options for construction.

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Bounds

Our original plot in Tutorial 2: Plotting data covers a spectral width of 16 ppm, but only around 7 ppm of the spectrum contains signals. As a refresher, these are the steps which we took to make it:

>>> import penguins as pg
>>> data_1d = pg.read(".", 1, 1)    # read in data
>>>
>>> data_1d.stage()                 # stage
>>> pg.mkplot()                     # construct
>>> pg.show()                       # display

It would probably be a good idea to only show the region between, say, 0.3 ppm and 7 ppm. To do this, we pass the bounds parameter to stage(). If you have the previous figure still open, close it first, and re-stage the dataset again. This will use the same dataset to make a new plot:

>>> data_1d.stage(bounds="0.3..7")
>>> pg.mkplot()
>>> pg.show()

In this example, we specified the bounds as a string {low}..{high}. The bounds can alternatively be specified as a tuple of numbers:

>>> data_1d.stage(bounds=(0.3, 7))    # same as above

If you do not want to specify a lower (or upper) bound, then omit it from the string, or pass None as one of the tuple components. The following handy table describes all the possibilities (the last case is equivalent to simply not passing the bounds parameter at all).

Region to be plotted	String form	Tuple form
Between 4 and 5 ppm	"4..5"	(4, 5)
Below 5 ppm only	"..5"	(None, 5)
Above 5 ppm only	"5.."	(5, None)
Entire spectrum	".."	(None, None)

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Colours and other aesthetics

The other major spectrum-specific options are aesthetic choices, such as colours, linewidths, and so on. The way stage() handles this is by taking keyword arguments and passing them along to matplotlib’s Axes.plot function (which penguins ultimately uses to draw the actual spectrum).

That means that any configuration option that you can pass to Axes.plot can also be passed to stage(). The full list of options is described in the matplotlib documentation, but some of the most commonly used ones are listed here.

• color: any of the formats listed in tutorials/colors/colors. If you don’t specify a colour, penguins will draw from the deep palette in the seaborn package.

• linewidth: a float. The default value is 1.

• linestyle: set to (for example) -- for a dashed line.

As a horrible example, let’s try using all of these options together:

>>> data_1d.stage(bounds="0.3..7", color="red", linewidth=0.5, linestyle="--")
>>> pg.mkplot()
>>> pg.show()