Plot size and resolution with R markdown, knitr, pandoc, beamer

I think that is a frequently asked question about the behavior of figures in beamer slides produced from Pandoc and markdown. The real problem is, R Markdown produces PNG images by default (from knitr), and it is hard to get the size of PNG images correct in LaTeX by default (I do not know why). It is fairly easy, however, to get the size of PDF images correct. One solution is to reset the default graphical device to PDF in your first chunk:

```{r setup, include=FALSE}
knitr::opts_chunk$set(dev = 'pdf')
```

Then all the images will be written as PDF files, and LaTeX will be happy.

Your second problem is you are mixing up the HTML units with LaTeX units in out.width / out.height. LaTeX and HTML are very different technologies. You should not expect \maxwidth to work in HTML, or 200px in LaTeX. Especially when you want to convert Markdown to LaTeX, you'd better not set out.width / out.height (use fig.width / fig.height and let LaTeX use the original size).

Figure sizes are specified in inches and can be included as a global option of the document output format. For example:

---
title: "My Document"
output:
  html_document:
    fig_width: 6
    fig_height: 4
---

And the plot's size in the graphic device can be increased at the chunk level:

```{r, fig.width=14, fig.height=12}          #Expand the plot width to 14 inches

ggplot(aes(x=mycolumn1, y=mycolumn2)) +     #specify the x and y aesthetic
geom_line(size=2) +                         #makes the line thicker
theme_grey(base_size = 25)                  #increases the size of the font
```

You can also use the out.width and out.height arguments to directly define the size of the plot in the output file:

```{r, out.width="200px", out.height="200px"} #Expand the plot width to 200 pixels

ggplot(aes(x=mycolumn1, y=mycolumn2)) +     #specify the x and y aesthetic
geom_line(size=2) +                         #makes the line thicker
theme_grey(base_size = 25)                  #increases the size of the font
```