Re-structures to include scripts from plotting episode.

Also:
- Reduces content of scripts episode
- Homogenises titles as strings instead of char arrays
- Homogenises code in command window with >>
- Gets rid of references to 'print'
- Saves figure reference

episodes/04-plotting.md

@@ -7,8 +7,10 @@ exercises: 10
 ::::::::::::::::::::::::::::::::::::::: objectives
 
 - Display simple graphs with appropriate titles and labels.
-- Get familiar with the functions `plot`, `heatmap` and `imagesc`.
+- Get familiar with the `plot` function.
+- Learn how to plot multiple lines at the same time.
 - Learn how to show images side by side.
+- Get familiar with the `heatmap` and `imagesc` functions.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
@@ -60,9 +62,9 @@ We need to give the figure a `title` and label the axes using `xlabel` and `ylab
 so that other people can understand what it shows
 (including us, if we return to this plot 6 months from now).
 ```matlab
->> title('Daily average inflammation')
->> xlabel('Day of trial')
->> ylabel('Inflammation')
+>> title("Daily average inflammation")
+>> xlabel("Day of trial")
+>> ylabel("Inflammation")
 ```
 
 ![](fig/plotting_average-inflammation.svg){alt='Average inflammation'}
@@ -74,21 +76,53 @@ Let's have a look at two other statistics: the maximum and minimum
 inflammation per day across all patients.
 ```matlab
 >> plot(per_day_max)
->> title('Maximum inflammation per day')
->> ylabel('Inflammation')
->> xlabel('Day of trial')
+>> title("Maximum inflammation per day")
+>> ylabel("Inflammation")
+>> xlabel("Day of trial")
 ```
 
 ![](fig/plotting_max-inflammation.svg){alt='Maximum inflammation'}
 
+:::::::::::::::::::::::::::::::::::::::::  callout
+
+## Scripts
+
+We often have to repeat a series of commands to achieve what we want, like with these plots.
+To be able to reuse our commands with more ease, we use scripts.
+
+A more in depth exploration of scripts will be covered on the next episode.
+For now, we'll just start by clicking `new->script`, using `ctrl+N`, or typing `edit` on the command window.
+
+Any of the above should open a new "Editor" window.
+Save the file inside the `src` folder, as `single_plot.m`.
+
+Alternatively, if you run
+```matlab
+>> edit src/single_plot.m
+```
+it creates the file with the correct path and name for you.
+
+**Note:** Make sure to add the `src` folder to your path,
+so that MATLAB knows where to find the script.
+To do that, right click on the `src` directory, go to "Add to Path" and to "Selected Folders". Alternatively, run:
+```matlab
+addpath("src")
+```
+
+Try copying and pasting the plot commands for the max inflammation on the script and clicking on the "Run" button!
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+Because we now have a script, it should be much easier to change the plot to the minimum inflammation:
+
 ```matlab
 >> plot(per_day_min)
->> title('Minimum inflammation per day')
->> ylabel('Inflammation')
->> xlabel('Day of trial')
+>> title("Minimum inflammation per day")
+>> ylabel("Inflammation")
+>> xlabel("Day of trial")
 ```
 
-![](fig/plotting_min-inflammation.svg){alt='Minumum inflammation'}
+![](fig/plotting_min-inflammation.svg){alt="Minumum inflammation"}
 
 These two are much more noisy than the mean, as we'd be expect.
 
@@ -98,16 +132,24 @@ It is often the case that we want to plot more than one line in a single figure.
 In MATLAB we can "hold" a figure and keep plotting on the same axes.
 For example, we might want to contrast the mean values accross patients
 with the inflammation of a single patient.
+
+Lets reuse the code we have in the script, but save it as a new script called "multiline_plot.m".
+You can do that using the dropdown menu on the save button, or by running this command on the terminal:
+```matlab
+>> copyfile("src/single_plot.m","src/multiline_plot.m")
+```
+and then open the new file with `edit src/multiline_plot.m`, as before.
+
 If we are displaying more than one line, it is important to add a legend.
 We can specify the legend names by adding `,DisplayName="legend name here"`
 inside the plot function. We then need to activate the legend by running `legend`.
 So, to plot the mean values we first do:
 ```matlab
 >> plot(per_day_mean,DisplayName="Mean")
 >> legend
->> title('Daily average inflammation')
->> xlabel('Day of trial')
->> ylabel('Inflammation')
+>> title("Daily average inflammation")
+>> xlabel("Day of trial")
+>> ylabel("Inflammation")
 ```
 
 ![](fig/plotting_average_inflammation_with_legend.svg){alt='Average inflamation with legend'}
@@ -138,9 +180,9 @@ The first part for the mean remains unchanged:
 ```matlab
 >> plot(per_day_mean,DisplayName="Mean")
 >> legend
->> title('Daily average inflammation')
->> xlabel('Day of trial')
->> ylabel('Inflammation')
+>> title("Daily average inflammation")
+>> xlabel("Day of trial")
+>> ylabel("Inflammation")
 ```
 
 Now we need to get the specific data for each patient.
@@ -174,35 +216,40 @@ It is often convenient to show different plots side by side.
 The [`tiledlayout(m,n)`](https://mathworks.com/help/matlab/ref/tiledlayout.html) command allows us to do just that.
 The first two parameter define a grid of `m` rows and `n` columns in which our plots will be placed.
 To be able to plot something on each of the tiles, we use the [`nexttile`](https://mathworks.com/help/releases/R2019b/matlab/ref/nexttile.html) command.
-For example, we can show the average daily min and max plots together with:
+
+Lets start a new script for this topic:
+```matlab
+edit src/tiled_plot.m
+```
+We can show the average daily min and max plots together with:
 ```matlab
 >> tiledlayout(1, 2)
 >> nexttile
 >> plot(per_day_max)
->> title('Max')
->> xlabel('Day of trial')
->> ylabel('Inflamation')
+>> title("Max")
+>> xlabel("Day of trial")
+>> ylabel("Inflamation")
 >> nexttile
 >> plot(per_day_min)
->> title('Min')
->> xlabel('Day of trial')
->> ylabel('Inflamation')
+>> title("Min")
+>> xlabel("Day of trial")
+>> ylabel("Inflamation")
 ```
 ![](fig/plotting_max-min-tiledplot.svg){alt='Max Min tiledplot'}
 
 We can also specify titles and labels for the whole tiled layout if we assign the tiled layout to a variable 
 and pass it as a first argument to `title`, `xlabel` or `ylabel`, for example:
 ```matlab
 >> tlo=tiledlayout(1, 2)
->> title(tlo,'Per day data')
->> xlabel(tlo,'Day of trial')
->> ylabel(tlo,'Inflamation')
+>> title(tlo,"Per day data")
+>> xlabel(tlo,"Day of trial")
+>> ylabel(tlo,"Inflamation")
 >> nexttile
 >> plot(per_day_max)
->> title('Max')
+>> title("Max")
 >> nexttile
 >> plot(per_day_min)
->> title('Min')
+>> title("Min")
 ```
 
 ![](fig/plotting_max-min-tiledplot-titles.svg){alt='Max Min tiledplot with shared labels'}
@@ -263,9 +310,9 @@ The [`heatmap` function](https://uk.mathworks.com/help/matlab/ref/heatmap.html)
 takes a table as input and produces a heatmap:
 ```matlab
 >> heatmap(patient_data)
->> title('Inflammation')
->> xlabel('Day of trial')
->> ylabel('Patient number')
+>> title("Inflammation")
+>> xlabel("Day of trial")
+>> ylabel("Patient number")
 ```
 
 ![](fig/plotting_heatmap.svg){alt='Heat map'}
@@ -278,9 +325,9 @@ Similarly, the [`imagesc` function](https://uk.mathworks.com/help/matlab/ref/ima
 represents the matrix as a color image. 
 ```matlab
 >> imagesc(patient_data)
->> title('Inflammation')
->> xlabel('Day of trial')
->> ylabel('Patient number')
+>> title("Inflammation")
+>> xlabel("Day of trial")
+>> ylabel("Patient number")
 ```
 
 ![](fig/plotting_imagesc-heatmap.svg){alt='imagesc Heat map'}
@@ -300,7 +347,7 @@ In our case, which one you use is a matter of taste.
 
 - Use `plot(vector)` to visualize data in the y axis with an index number in the x axis.
 - Use `plot(X,Y)` to specify values in both axes.
-- Document your plots with `title('My title')`, `xlabel('My horizontal label')` and `ylabel('My vertical label')`.
+- Document your plots with `title("My title")`, `xlabel("My horizontal label")` and `ylabel("My vertical label")`.
 - Use `hold on` and `hold off` to plot multiple lines at the same time.
 - Use `legend` and add `,DisplayName="legend name here"` inside the plot function to add a legend.
 - Use `tiledlayout(m,n)` to create a grid of `m` x `n` plots, and use `nexttile` to change the position of the next plot.