[R-sig-teaching] Choice of graphics package

[Randall Pruim]

When I run your code, the colors in my plot are not set to the colors chosen unless I do

ggplot(mtcars, aes(x = hp, fill = factor(gear))) + geom_bar() + scale_discrete

Did your code example really work for you?

I think the point is that lattice and ggplot2 differ in terms of what is called part of the theme.  In lattice, the colors used for discrete variables are part of the theme, and so can be included in the global default.  In ggplot2, they are not part of the theme and cannot be set with theme_set().

I get that you can save your scales information as an object and add it on to any plot so you only have to specify the colors (or whatever) once.   But I think you still need to add the scale information onto each plot.

—rjp


On Nov 27, 2015, at 9:18 PM, Ista Zahn <istazahn at gmail.com<mailto:istazahn at gmail.com>> wrote:

Woops, messed up the example! I meant

theme_set(theme_bw() +
         theme(rect = element_rect(fill = "gray10")))

scale_discrete <- scale_fill_manual(values = c("orange", "purple",
"pink", "cyan"))

ggplot(mtcars, aes(x = hp, fill = factor(gear))) + geom_bar()

i.e., the whole point is you don't need to add this stuff to every plot.

Best,
Ista

On Fri, Nov 27, 2015 at 9:13 PM, Ista Zahn <istazahn at gmail.com<mailto:istazahn at gmail.com>> wrote:
Hi Randal,

To be honest I don't know the lattice theme system at all, so it is
entirely possible that you can easily do things there that are more
complicated in ggplot2. However, it is easy to set theme and scale[1]
defaults in ggplot2, e.g.,

library(ggplot2)

theme_set(theme_bw() +
         theme(rect = element_rect(fill = "gray10")))

scale_discrete <- scale_fill_manual(values = c("orange", "purple",
"pink", "cyan"))

ggplot(mtcars, aes(x = hp, fill = factor(gear))) + geom_bar() +
 theme_bw() +
 scale_fill_manual(values = c("orange", "purple", "pink", "cyan"))


Best,
Ista

[1] In ggplot2 theme elements are distinct from scales, and AFAIK they
have to be set separately.

On Fri, Nov 27, 2015 at 6:24 PM, Randall Pruim <rpruim at calvin.edu<mailto:rpruim at calvin.edu>> wrote:

On Nov 27, 2015, at 3:37 PM, Ista Zahn <istazahn at gmail.com<mailto:istazahn at gmail.com>> wrote:

(Theming in ggplot2 generally requires you to do something to each plot,
one of the downsides of ggplot2.)

That is completely untrue. Whatever downsides ggplot2 may have, this is not
one of them.


Ista,

My guess is that you didn’t understand my claim.  Either that or you know
something about ggplot2 that I’ve not been able to locate anywhere.  (Since
Hadley is on  this list, he can chime in if I’m missing something.)

So let me explain what I mean with an example.

Suppose I want to create six plots of various sorts.  Each of them uses
color according to a factor a with three levels.  That's groups = a in
lattice and colour = a in ggplot2.  So far so good.

But after I have created all of these plots with the default color choices,
I decide I want to have the colors be blue, red, and 50% gray.  In lattice,
I can put this information into the default theme with

trellis.par.set( superpose.symbol = list(col = c("blue", "red", "gray50")) )

and without any adjustments to any of the plotting code, all the plots will
update to the new color scheme.   show.settings() will even show me what my
default theme looks like.

One line of code changes in one place and all the plots are using the new
color scheme.  And if my new choices are choices I will use frequently, I
can put the theme into a package and do something like

trellis.par.set(theme = theme.mosaic())

There is also the option to add these themes to individual plots using the
par.settings argument — this is more like the ggplot2 way.

In ggplot2, I need to add on scale_colour_manual() to EACH PLOT, or write
some sort of wrapper that does the job for me.  In either case, if I started
out using the defaults and want to make document-wide changes, I need to
edit EACH plot to get the desired affect.  In lattice, this is one line of
code and all the plots are good to go.

Last I looked for this, ggplot2 did not provide a way to set these sorts of
defaults and generally prefers a system where all of this sort of theming is
located local to each plot.  So plots end up having a bunch of theme stuff
added on to them like

+ theme_minimal()
+ scale_colour_manual(values = c(“blue”, “red”, “gray50”)
+ etc.

See the examples at

http://docs.ggplot2.org/dev/vignettes/themes.html

Especially for teaching, I find this to be a real problem.  I don’t want to
clutter up early examples with all this sort of formatting, but I do want to
control the choice of colors used so that they work well for printing or
projecting in my local environment.  When I’m producing a journal or some
other sort of report, this is less important because I generally don’t show
the code in the final document — only the plot.  But it still violates the
DRY principle (Don’t Repeat Yourself).

—rjp

PS.  I should have mentioned one commonly held, but poorly justified, reason
to prefer ggplot2 over lattice:  the default colors.  lattice makes it easy
to adjust the defaults.  latticeExtra even provides a ggplot2 look-alike
theme that will make your lattice plots look a lot like ggplot2 plots.  (The
won’t match exactly because they don’t include all of the same elements.
Liking elements available in one system but not in the other is a possible
reason to prefer one over the other.)  On the other hand, if you don’t like
the defaults in ggplot2 — you’re out of luck, you don’t get the change the
defaults.






	[[alternative HTML version deleted]]