Lesson Navigation
- Introduction, Overview of the MATLAB GUI, and Setup
- Variables and Arrays
- Plotting Data
- Scripts
- Loops
- Conditional Statements
- Custom Functions
MathWorks MATLAB is a complete interactive desktop environment and programming language. MATLAB is used by Mathematicians, Scientists, Engineers and others for numeric computation, data analysis, data visualization, and creation of applications. There are a variety of MATLAB add-on toolboxes for solving specific problems, for example, in computational biology or image processing.
MATLAB has excellent documentation, support, and user created forums and learning materials. Here are a few recommended resources:
- MathWorks MATLAB Documentation
- MathWorks MATLAB Tutorials
- MATLAB Central User Community
- Stackoverflow MATLAB Questions
- Software Carpentry Programming with MATLAB
We also have many MATLAB eBooks available from The University of Alabama Libraries. Try a Scout search for Matlab in the record title and limit to eBooks:
TI (Matlab) AND PT eBook AND FT Y
The University of Alabama maintains a site license to MATLAB and Simulink, as well as many of the add-on toolboxes. See the UA Office of Information Technology website for access and installation instructions. MATLAB is available for Windows, Mac, and Linux.
Windows and Mac users can open MATLAB similarly to other installed programs. Linux users will need to open a terminal window and type matlab to launch MATLAB.
user@computer:~$ matlab
MATLAB has a tabbed toolbar interface and four main windows:
- Current Folder: For file directory viewing and navigation
- Command Window: For entering and executing MATLAB commands. Users input commands at the MATLAB prompt,
>>, and then execute with theEnterkeyboard button. - Editor: Allows input of multiple lines of code and sequential execution, which is useful for running scripts.
- Workspace: For viewing stored variables.
MATLAB has many built in features and functions, so it is important to know how to access documentation and help from within MATLAB. You can access the documentation reference pages directly from the MATLAB toolbar or from the Command Window using doc:
>> doc
The doc function will open the MATLAB documentation in a new window browser. You can search the documentation with the docsearch function from the Command Window, for example, if we wanted to find all documentation pages mentioning histogram:
>> docsearch histogram
MATLAB also contains help entries for functions and these can be viewed with help. For example, if we wanted to view help for the mean function:
>> help mean
mean Average or mean value.
S = mean(X) is the mean value of the elements in X if X is a vector.
For matrices, S is a row vector containing the mean value of each
column.
...
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...Finally, we can search the help entries with lookfor. Below, we find all functions containing the word plot:
>> lookfor plot
cellplot - Display graphical depiction of cell array.
etreeplot - Plot elimination tree.
gplot - Plot graph, as in "graph theory".
treeplot - Plot picture of tree.
plot - Alpha shape plot
plot - Plot a polyshape object
odeplot - Time series ODE output function.
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...Should you use Documentation or Help? Use both!
We will be using a text file dataset, CID51840_similar.txt, for a few of the examples during the workshop. The easiest way to get this file setup is probably to download this GitHub Repository as a zip file, then unarchive the zip file. Finally, copy the MATLAB Mdata folder (UALIB_Workshops/01_MATLAB_fall_2020/Mdata) to a convenient location such as your desktop. After copying thee Mdata folder to your desktop, open MATLAB, and change the working directory in the Command Window to the Mdata folder path:
>> cd('/home/myusername/Desktop/Mdata')
There are many different ways to import data into MATLAB. We will use the readtable function. The readtable function creates a table from delimited text files and other formats like .xls and .ods.
>> myCIDdata = readtable('CID51840_similar.txt','Format','%s %s %s %f %d %d %d')
myCIDdata =
574×7 table
IsomericSmiles CID MolecularFormula MolecularWeight RotatableBondCount HeavyAtomCount AtomChiralCount
_____________________________________________________________________ _____________ _________________ _______________ __________________ ______________ _______________
{'CCN(CC(=O)C)C(C1=CC=CC=C1)C(=O)OC(C)(C)C' } {'146168522'} {'C17H25NO3' } 291.4 8 21 1
{'CCN(CC(=O)OCC)C(C1=CC=CC=C1)C(=O)OC' } {'146168519'} {'C15H21NO4' } 279.33 9 20 1
{'C1=CC=C(C=C1)CN(CC2=CC=CC=C2)C(C3=CC=C(C=C3)F)C(=O)O' } {'146161459'} {'C22H20FNO2' } 349.4 7 26 1
{'CC.CCCN1CCN(CC1)C(C2=CC=CC=C2CC)C(=O)O' } {'145524776'} {'C19H32N2O2' } 320.5 6 23 1
{'CC.CC.CCC.CC(=C)N1CCN(CC1)C(C2=CC=CC=C2)C(=O)O' } {'145520251'} {'C22H40N2O2' } 364.6 4 26 1
{'CC.CC(C)N(C)C(CC1=CC=CC=C1)C(=O)O' } {'145086414'} {'C15H25NO2' } 251.36 5 18 1
{'CN(C)C(C1=CC=CC=C1C(F)(F)F)C(=O)O.Cl' } {'144259917'} {'C11H13ClF3NO2'} 283.67 3 18 1
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...The above command imports the data within the CID51840_similar.txt file using the built in MATLAB readtable function and then saves the data as a variable called myCIDdata. The format option was added in order to specify the data type format for each of the seven columns. %s is a character vector, %f is a floating point number, and %d is an integer. The data is a collection of molecules that are similar to PubChem Compound Identifier (CID) 51840. The molecules are represented in a linear notation called SMILES and some associated data is included about the molecules such as their molecular weight and heavy atom counts. It is not necessary that you fully understand what this data represents, but rather understand that it is tabular data with a mixture of character and numeric data.
Attribution
Content in this workshop have been adapted and derive from the Software Carpentry Programming with MATLAB lesson (CC BY 4.0 license for Instructional Materials and MIT License for programs and code examples). In general, we reused parts of their lesson including the basic structure, some descriptions, and logical ordering, but included our own specific variables, scripts, loops, and custom function examples. We have maintained the MIT license for program and code examples. Molecular dataset examples were retrieved from NCBI via their EDirect utility and is credited to NCBI and NLM. Please see the NCBI Website and Data Usage Policies and Disclaimers for more information regarding the data.