[r] Plot size and resolution with R markdown, knitr, pandoc, beamer

Doesn't fit on the slide by default, doesn't even print by any other means.

Here's the .Rmd: Edit: it seems you have to use plot() in every chunk. Second plot now prints.

# Plot should show at high resolution

```{r echo=FALSE, comment = ""}
# load some data
require(plyr)
rbi <- ddply(baseball, .(year), summarise,  
  mean_rbi = mean(rbi, na.rm = TRUE))
```

```{r}
# plot
plot(mean_rbi ~ year, type = "l", data = rbi)
```

# Second attempt
```{r, fig.width = 2, fig.height = 2}
plot(mean_rbi ~ year, type = "l", data = rbi)
```

# Third attempt
```{r, out.width = 2, out.height = 2}
plot(mean_rbi ~ year, type = "l", data = rbi)
```

# Fourth attempt
```{r, out.width = '200px', out.height = '200px'}
plot(mean_rbi ~ year, type = "l", data = rbi)
```

# Fifth attempt
```{r, out.width = '\\maxwidth'}
plot(mean_rbi ~ year, type = "l", data = rbi)
```

Save that as test.Rmd Then compile to tex using beamer:

knit("test.Rmd")
system("pandoc -s -t beamer --slide-level 1 test.md -o test.tex")

Open test.tex in RStudio and click "Compile PDF".

I've read Yihui's documentation and hope I haven't missed something really obvious.

Edit new code incorporating Yihui's suggestions.

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

# Plot should show at high resolution

```{r echo=FALSE, comment = ""}
# load some data
require(plyr)
rbi <- ddply(baseball, .(year), summarise,  
  mean_rbi = mean(rbi, na.rm = TRUE))
```

```{r}
# plot
plot(mean_rbi ~ year, type = "l", data = rbi)
```

# Second attempt
```{r, fig.width = 4, fig.height = 4}
plot(mean_rbi ~ year, type = "l", data = rbi)
```

sessionInfo()

 R version 3.0.1 (16/05/2013)
Platform: x86_64-pc-linux-gnu (64-bit)

Local:
 [1] LC_CTYPE = en_US.UTF-8 LC_NUMERIC = C LC_TIME = C LC_COLLATE = C        
 [5] LC_MONETARY=C        LC_MESSAGES=C        LC_PAPER=C           LC_NAME=C           
 [9] LC_ADDRESS=C         LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C 

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] plyr_1.8       markdown_0.6   knitr_1.2      rCharts_0.3.51 slidify_0.3.52

loaded via a namespace (and not attached):
 [1] RJSONIO_1.0-3   codetools_0.2-8 digest_0.6.3    evaluate_0.4.3  formatR_0.8    
 [6] grid_3.0.1      lattice_0.20-15 stringr_0.6.2   tools_3.0.1     whisker_0.3-2  
[11] yaml_2.1.7  

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
```