knitr/rmarkdown - reducing html file size

To prevent scatterplots with many points blowing up the size of your vector graphics (and accordingly html output) you can use geom_point_raster() from the ggrastr package. Eat the cake and have it too!

Following the suggestion of @daroczig to use the "dpi" knitr chunk option, I modified your code as follows (see below).

• You had set the dev chunk option equal to "svg", which produces very large vector graphics files, especially for images made up of many elements (points, lines, etc.)
• I set the dev chunk option back equal to "png", which is the default raster graphics format for HTML output. So you don't need to touch it at all. Keeping the dev chunk option equal to "png" dramatically reduces the HTML output file size.
• I set the dpi chunk option equal to 36 (72 is the default), to lower the image resolution, and decrease the HTML output file size further.
• I set the out.width and out.height chunk options equal to "600px", to increase the image dimensions.
• You can change the dpi, out.width, and out.height options, until you get the HTML output file size and the image dimension to what you want. There's a trade-off between output file size and image resolution.

After knitting the code, I got an HTML output file size equal to 653kB, even when plotting 5e4 data points.

---
title: "Change size of output HTML file by reducing resolution of plot image"
author: "My Name"
date: "September 7, 2015"
output: html_document
---

```{r}
# load ggplot2 silently
suppressWarnings(library(ggplot2))
# chunk option dev="svg" produces very large vector graphics files
knitr::opts_chunk$set(dev="svg")
# chunk option dev="png" is the default raster graphics format for HTML output
knitr::opts_chunk$set(dev="png")
```

```{r, dpi=36, out.width="600px", out.height="600px"}
# chunk option dpi=72 is the default resolution
set.seed(1)
mydf <- data.frame(x=rnorm(5e4),y=rnorm(5e4))
ggplot(mydf, aes(x,y)) + geom_point(alpha=0.6)
```