Week 12: Creating an R Markdown File for Alignment Score Visualization

Creating the R Markdown file "Alignment Score Visualization" was a great learning experience. It allowed me to combine R code, text, and visuals in one document, which is both easy to read and share. Here’s what I learned and how it went:

Getting Started

At first, R Markdown felt a bit confusing because it combines text and code in one file. But once I understood the structure, it became clear how powerful it is. The key was using code chunks, which are sections of the file that run the R code. Each chunk starts with ```{r} and ends with ```.

For my project, I wanted to display alignment scores for V and J regions in a table and a bar chart. Writing and organizing the code into chunks made it easy to run and test each part.

Challenges I Faced

Code Showing as Plain Text:
When I first tried knitting the file, the HTML output only showed the code as plain text. I realized this was because I had included everything in the setup chunk, which is only for settings. Separating the data and visualization code into their own chunks fixed this.

Troubleshooting Errors:
Debugging code in R Markdown was tricky because knitting stops when there’s an error. To fix this, I ran each chunk one by one in RStudio before knitting the whole file. This made it easier to find and fix mistakes.
Deciding What to Show:
I learned that I could control whether the code or just the results showed up in the final document. For the table, I wanted both the code and output to show, so I used echo = TRUE. For the bar chart, I hid the code (echo = FALSE) so the focus was on the visualization.

What I Learned

R Markdown Is Powerful:
It’s a great tool for combining text, code, and results in one document. It makes it easy to share your work in a clear and professional way.
The Importance of Code Chunks:
Properly setting up code chunks is key. Using options like echo, eval, and include helped me decide what to show in the final file.
Data Visualization with ggplot2:
Creating the bar chart with ggplot2 was simple and fun. I learned how to make clear, customizable visualizations that look professional.

Reflection

I’m pretty happy with how this project turned out. It showed me how useful R Markdown is for combining analysis, text, and visuals. In the future, I plan to use R Markdown for more projects, try new output formats like PDF, and even add interactive visualizations.

If you’re new to R Markdown, I recommend starting with a small project like this. It’s a great way to learn how to present your work effectively.

For a more detailed exploration visit my GitHub repository

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