MIC plot theme

[theanita1]

Hi Matthijs (or anyone else who can answer my question)

On the website the MIC plots display quite nicely - white background, black around the bars etc,
However when I use the autoplot function it comes back with the typical R formatting

Should I need additional ggplot coding to achieve the same output as what's displayed on the instructions?
edit
If yes would you mind sharing the additional required code?
I can't manage to get the same output with my current ggplot knowledge

[msberends]

Dear @theanita1,

There is no additional code required, since the website uses exactly the code that precede the plots (that should at least be the case...). So, for example:

my_mics <- random_mic(100)
ggplot2::autoplot(my_mics,
                  mo = "Escherichia coli",
                  ab = "ampicillin",
                  guideline = "EUCAST 2021")

Can you reproduce this? Which plots are you referring to from the website?

[theanita1]

Hi Matthijs,
I'm referring to the plots on this page
Particularly the ones that look like this:

The x-axis is removed, the y-axis is clean, the background is plain and the boxes are outlined. Additionally the legend spans across the top rather than on the side of the graph

[msberends]

Ahhh, but that's not ggplot 😉 That's base R.

I wrote something to get to similar results in ggplot for you:

ggplot2::autoplot(random_mic(100),
                  mo = "Escherichia coli",
                  ab = "ampicillin",
                  guideline = "EUCAST 2021") +
  # here starts the theme part
  ggplot2::theme_minimal() + 
  ggplot2::theme(panel.grid = ggplot2::element_blank(), 
                 axis.line.y = ggplot2::element_line(linewidth = 0.25), 
                 legend.position = "top")

Or you could create your own function to reduce code:

our_theme <- function(...) {
  ggplot2::theme_minimal() + 
    ggplot2::theme(panel.grid = ggplot2::element_blank(), 
                   axis.line.y = ggplot2::element_line(linewidth = 0.25), 
                   legend.position = "top",
                   ...)
}

# and now just add our_theme() to your future code (works with any ggplot):
ggplot2::autoplot(random_mic(100),
                  mo = "Escherichia coli",
                  ab = "ampicillin",
                  guideline = "EUCAST 2021") +
  our_theme()

[theanita1]

Thanks for that - still learning the in's and out's of R so I appreciate the feedback and code!