R help - Jul 2021 - Plotting confidence intervals with ggplot, in multiple facets.

Rolf,

Your example shows two plots with one above the other.

If that is what you want, then a solution like the one  Jeff provided  using
facet_grid() to separate data based on the parameter value. It also scales
up if you add additional sets of data for gamma and delta up to a point.

An alternative to consider if your ggplot wizardry has not kicked in, or if
your need is to connect more diverse plots into a sort of collage, is to
make multiple plots and save them as in:

P1 <- ggplot(...) ...
P2 <- ggplot(...) ...

Each of these two or more plots can operate on whatever data you supply it.
In your case, you would filter the rows that have the values you want.

Then you can use one of many packages out there such as cowplot or gridextra
to consolidate the parts as in:

plot_grid(P1, P2)

Or 

grid.arrange (P1, P2)

These other functions vary in functionality but many allow you to adjust how
many rows or columns you want or the relative sizes of the subplots and so
on. Some allow you to create output into things like a PDF where parts spill
over well into additional pages.

I note one think Jeff did not replicate. If you want that in your output,
use geom_hline as shown below:

ggplot(dta,aes(x=Ndat,y=estimate, ymin=lower,ymax=upper))+
  geom_point() +
  geom_errorbar(width=30) +
  geom_hline(yintercept = 0, color="red") +
  facet_grid(param~1)

Personally, I sometimes adjust the limits to make a graph truly start at
zero but in your case you can have error bars being displayed with parts
below zero so showing where zero is graphically can be useful.




-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Rolf Turner
Sent: Sunday, July 18, 2021 2:17 AM
To: r-help at r-project.org
Subject: [R] Plotting confidence intervals with ggplot, in multiple facets.



I have need of creating a plot displaying confidence intervals (for the mean
bias in parameter estimates) with one panel or facet for each of the two
parameters in question.

I can do this in base R graphics, but the result is not as aesthetically
pleasing as I would like.  I have attached an example graphic in the file
"eg.pdf".

I would like to try using ggplot2, but cannot get my head around the syntax.
(Life is a struggle when one is old and senile!)  I have been shown in the
past how to produce a single-facet plot of such confidence intervals,
basically using the geom_errorbar() function, but I cannot see how to
produce multiple facets, depending on a "param" factor.  I have
thrashed
around a bit but after succeeding in only confusing myself, I thought I
would save wear and tear on my brain by asking this list.  I'm sure the
answer is pretty simple, but I'm just too stupid to see it.

Can anyone give me a recipe for creating, with ggplot(), a graphic like unto
that shown in "eg.pdf", but prettier?  I have attached the data that
were
used to create "eg.pdf" in the form of a data frame, in a file called
"egData.txt".  This file was produced by dput() so read it in using
dget("egData.txt").

With eternal gratitude.

cheers,

Rolf Turner

--
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

Thanks to Jeff Newmiller, Rui Barradas and Avi Gross for their
extremely helpful replies.  I have got both Jeff's and Rui's code to
run.  I am currently experimenting with Avi's suggestion of producing
multiple plots and then putting them together using plotgrid() or
grid.arrange().  This idea seems to me to be most promising in terms of
a desideratum that the y-axis scales/limits should be different on the
two facets.  Also the y-axis labels.

And speaking of y-axis labels:  is it possible in ggplot() to get
mathematical notation in axis labels, titles and possibly other
annotation?  (In the manner of plotmath() in base R graphics.)
Specifically I'd like to get the Greek letters alpha and beta in the
y-axis labels.  In base R graphics I'd do something like
ylab=expression(paste("bias in ",beta)) .  Is there an appropriate
analogue in ggplot()?  (I think that I may have asked this question
before, some time back, but have forgotten the answer.)

cheers,

Rolf

P.S.  The following is kind of apropos of nothing, but it might serve as
a useful warning to others of a Trap for Young Players.  I nearly went
mad (madder?) for a very long time when trying to get Rui's code to run.
I kept getting errors of the form:
> Error in source("scr.Rui") : scr.Rui:6:2: unexpected input
> 5: ggplot(eg, aes(Ndat, estimate)) +
> 6:  ?
>     ^
Took me an unconscionably long while to figure out what was going on.
I could not see why Jeff's code ran without problem, while Rui's (which
was very similar) fell over.  Turns out the second character in the
offending line is a non-printing character, the 160th member of the
ASCII character set. (It can be produced using "\u00A0".)  Apparently
this is a "non-breaking space". Whatever that means.  It does NOT get
treated as white space in the usual way, and triggers the foregoing
error.

Presumably this invisible character got introduced, into the code that
Rui emailed, by one of the (many!) infuriating idiosyncrasies of
Windoze.  Yet another reason, among the many millions of such, not to
use Windoze.

R.

-- 
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276