R ggplot: colour and fill arguments

Question

I am new in R and just started to learn ggplot. I am so confused by the syntax, I thought the "color" and "fill" arguments should always follow color names or RGB specifications. But I've seen many cases where "color" and "fill" in aes() were assigned with variables, see the below example.

ggplot(faithfuld, aes(waiting, eruptions)) +
  geom_raster(aes(fill = density))

I couldn't find an explanation of such use in [R documentation][1]. What does it mean? coloring by factor/grouping? if fill and color are assigned with variables, where should colors be specified? in scale_colour_manual?

Besides, I noticed that if specifying colors and/or transparency in aes(), the specified colors or transparency won't realise. For instance, in the below code, alpha = 0.3 is not working, I can change the alpha to any value, and the transparency will always be 0.5 in plotting. Why is that?

Also, I noticed that if I deleted fill or alpha in the aex(), the following "scale_fill_manual" wouldn't work. So is it true that "scale_fill_manual" is dependent on the geom_xx()?

p <- ggplot(dfcc) + geom_ribbon(aes(x = yr, ymax = ciupper, ymin = cilower, fill = "", alpha = 0.3)) +
  scale_fill_manual(values = "blue", labels = "CI95%") 

Sorry for so many questions, I am just so confused, and any help will be appreciated! [1]: https://search.r-project.org/CRAN/refmans/ggplot2/html/aes_colour_fill_alpha.html

Answer 1

Please read Chapter 3 of R for Data Science when you got some time, it may answer your question (Section 3.3):

You can convey information about your data by mapping the aesthetics in your plot to the variables in your dataset.

As examples, please see and observe the differences among these 3 set of code and their outputs:

1. Use Red as color:

   iris |> 
     ggplot(aes(x = Sepal.Length, y = Sepal.Width)) +
     geom_point(color = "red") +
     theme_minimal() +
     theme(panel.grid = element_blank())
   

   You get:

   

2. Use Species as color:

   iris |> 
     ggplot(aes(x = Sepal.Length, y = Sepal.Width)) +
     geom_point(aes(color = Species)) +
     theme_minimal() +
     theme(panel.grid = element_blank())
   

   You get:

   

3. Modify Species with the color of your choice:

   iris |> 
     ggplot(aes(x = Sepal.Length, y = Sepal.Width)) +
     geom_point(aes(color = Species)) +
     theme_minimal() +
     theme(panel.grid = element_blank()) +
     scale_color_manual(values = c("red", "yellow", "purple"))
   

   You get: