## Week 3 Problem Set

a)  **An R Markdown file is plain text file that contains what 3 important types of content?**

The 3 types on content are headers, code chunks, and text. The output of the code will be displayed directly below the code chunk.

b)  **What is a chunk and how do you add them? of the many chunk options which one do you think you will use the most and why? How is inline code different than code chunks?**

You add chunks in several ways but the most important ones are Cmd/Ctrl + Alt + I or just typing in ``` {TYPE CHUNK_NAME OPTIONS} ...code here... ``` where TYPE and OPTIONS refers to the chunk options and CHUNK_NAME allows you to easily access chunks in other sections of the document. We'll principally be using r as the language type, but you could also use bash or python. There are also around 60 options that you can use to customize the chunk. "eval=FALSE" is an easy way to disable a chunk of code not being used. "include=FALSE" can also be useful to hide sections of code - like when all the libraries are loaded in. 

Code chunks will display their output below them, making them different from inline code.


c)  **What’s gone wrong with this code? Why are the points not blue?**

```
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy, color = "blue"))
```

Here, the color tag is applying a different color to all the labels, not choosing a specific color. The label here is "blue", and since there's no actual label, it decides everything is called "blue" - hence the dots being labelled "blue" in the legend.


d)  **Of the many things we have done in class the past two weeks, what is one aspect you would like to revisit and spend more time on?**

I would be interested in discussing some of the statistics used in the "Fitting Multifactorial Models of Differential Expression" article".