Graphviz Usage

When developing software, whether for presentation or to organize thoughts, using flowcharts is often necessary. Instead of using a drawing board or Word, which can be time-consuming when the diagram becomes complex and needs frequent updates, a tool like Markdown that allows you to focus on content rather than form is very important.

Graphviz is a script-based graph visualization tool that can create many types of graphs. Currently, I only use flowcharts. To create a flowchart, you need to write a .dot formatted file, which looks like this:

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16

digraph workflow{
    // Default definition section for the entire graph
    label = "Workflow For Mutation Call"
    node[shape = box]

    // Definition section for nodes in the graph
    raw [label="Raw Bam"];
    clean [label="UMI Dedup Bam"];
    align [label="Split Bam"];
    vcf [label="Disc Bam(Prototype)"];

    // Relationship section for the flowchart
    raw -> clean [label="fastp"];
    clean -> align [label="bwa"];
    align -> vcf [label="GATK Mutect2"];
}

I divided the above code into three parts:

• The first part sets default properties for elements in the graph, such as label which is the title of the graph, and node which defines the nodes in the flowchart. I set the default node shape to a box (the default is a circle).
• The second part defines the nodes in the graph by specifying what nodes there are and then customizing them in the brackets, such as label to specify the displayed text.
• The third part defines the order of relationships in the flowchart, such as raw -> clean which draws an arrow from raw to clean. Similarly, you can customize it with brackets.

After writing the above code, you can generate images by calling the dot command of Graphviz:

1

dot -Tpng workflow.dot > workflow.png

There is a corresponding plugin for VSCode, and on Linux, after installing the plugin, you can preview flowcharts as you write, which is very convenient.
```