[R] ggplot does not show in knitr

[R. Michael Weylandt]

See R FAQ 7.22 for the gory details -- It needs to go around the
qplot() statement.

In interactive use, most objects are "printed" after evaluation:
sometimes this doesn't happen because the returned value is marked
invisible. For grid graphics objects (of which ggplot objects are a
type), this "printing" is the actual display mechanism. This makes
lots of sense in a interactive context because after the object is
assembled, it is auto-printed back to you, and hence displayed.

However, inside a for loop (and a few other cases) the auto-printing
is turned off. For example

2 + 2 # will display 4

for(i in 1:10) 2 + 2 # Will not print 4 ten times

To get printing behavior in a for loop, you need to print explicitly:

for(i in 1:10) print(2+2) # Will print 4 ten times.

AFAICT, knitr turns on the regular auto-printing, but it doesn't get
the printing inside the for loop (perhaps because there's no mechanism
to make it always happen, but that's just idle speculation)

Hope this helps,
Michael

On Thu, Aug 2, 2012 at 3:52 PM, firdaus.janoos <fjanoos at bwh.harvard.edu> wrote:
> Could you elaborate on this ? Where would the print /plot statement go ?
>
>
> On Thu, Aug 2, 2012 at 4:38 PM, Michael Weylandt
> <michael.weylandt at gmail.com> wrote:
>>
>> You need to explicitly print() the graphs to make them show -- or in
>> recent ggplot2 versions I think you can also use plot() as an alias.
>>
>> Michael
>>
>> On Aug 2, 2012, at 2:37 PM, "firdaus.janoos" <fjanoos at bwh.harvard.edu>
>> wrote:
>>
>> > Hello,
>> >
>> > I'm having some issues getting a ggplot figure to show up in the knitr
>> > output, when placed in a loop.
>> >
>> > Specifically, I have a loop inside a knitr chunk :
>> >
>> > ```{r fitting, warning=FALSE, fig.width=10, fig.height=10,
>> > fig.keep='high'}
>> > for (t in 1:T)
>> > {
>> >      # do a regression of tgt.vals ~ predictors and compute coeffs and
>> > fitted values (fit.vals / fit.adj.vals)
>> >
>> >    plot( x=tgt.vals, y=fit.vals );
>> >    plot( x=tgt.vals, y = fit.adj.vals );
>> >
>> >    qplot( x = pred.names, y = coeffs);
>> >
>> > }
>> >
>> > ```
>> >
>> > The html output file shows the output of first 2 plot commands but not
>> > that
>> > of the qplot command. Even if i remove the 2 plots and keep only the
>> > qplot
>> > in the loop, it does not display in the html output.
>> > The qplot just by itself, not in a loop, displays fine. Also, there are
>> > no
>> > issues when I run in regular R.
>> >
>> > Any suggestions of what is going on ?
>> >
>> >    [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> > http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>
>