Hi
Jonathan R. Blaufuss wrote:
Paul, You solution worked out really well when I ran my code in R.
However, when I try to turn the plot into a pdf, the unicode string
no longer seems to function and instead of the sigma symbol there are
just two periods (See example code below).
The following is the code working in the R environment just like I
want it to look:
set.seed(1)
> Data=rnorm(100,sd=10000)
> plot(density(Data))
text(25000,0.00004,
> paste("\u03c3 = ",
> format(round(sd(Data),digits=3),big.mark=",")),
> font=2, col="blue")
Now when I try to turn the plot into a pdf, the sigma symbol no
longer appears. It is replaced by two periods.
pdf(file="C:/Rquestion.pdf")
> ### Note: You can choose a place for this file to be saved
> set.seed(1)
> Data=rnorm(100,sd=10000)
plot(density(Data))
> text(25000,0.00004,
> paste("\u03c3 = ",
format(round(sd(Data),digits=3),big.mark=",")),
> font=2, col="blue")
dev.off()
Is it possible to make the unicode string function when writing to a
pdf or do I need to form the sigma symbol some other way?
Here are a few suggestions (roughly in increasing order of complexity) ...
1.
The standard symbol font for PDF is actually quite "heavy", so you could
try just doing the original plotmath approach. Even though the sigma
symbol is not bolded, it stands up reasonably well next to the bold
digits (in PDF).
pdf(file="RquestionDefault.pdf")
set.seed(1)
Data=rnorm(100,sd=10000)
plot(density(Data))
text(25000,0.00003,
bquote(bold(sigma==.(mySigma)),
list('mySigma'=format(round(sd(Data),digits=3),
big.mark=","))),
col='blue')
dev.off()
2.
The problem that you are seeing with the two dots in PDF is due to the
fact that the (multibyte) Unicode sequence "\u03c3" has to be converted
to a single byte "encoding" to be stored in the PDF file.
Unfortunately, the default encoding (ISOLatin1) does not contain the
'sigma' character, so the conversion fails (hence the dots). You can
specify an encoding that does contain the 'sigma' character, e.g.,
CP1253, but you also need to use a *font* that contains the 'sigma'
character. Here's an example of this solution that just uses the
standard fonts that R knows about ...
pdfFonts(stdsym=Type1Font("standardsymbol",
c("Helvetica.afm",
"s050000l.afm",
"Helvetica-Oblique.afm",
"Helvetica-BoldOblique.afm",
"Symbol.afm"),
encoding="CP1253"))
pdf("RquestionEncSym.pdf")
set.seed(1)
Data=rnorm(100,sd=10000)
plot(density(Data))
text(25000,0.00004,
paste("\u03c3 = ",
format(round(sd(Data),digits=3),big.mark=",")),
family="stdsym", font=2, col="blue")
dev.off()
What this is doing is specifying a new font "family" that has the
standard symbol font in the place where you would normally have the bold
font. Note that the encoding for this font is CP1253. This new font
family is then specified in the call to text(..., family="stdsym").
There are two unsatisfactory aspects to this solution: the sigma symbol
is still not bold (it is in fact just the same symbol as for solution
1), PLUS the digits are now not bold either. So this is not really a
very good solution, but it demonstrates some of the ideas we need to get
a better solution.
3.
The problem with the previous solution is that it used the standard
symbol font for the entire piece of text that was being drawn (the sigma
symbol and the digits). If we go back to using plotmath expressions, we
can improve on this because plotmath allows us to use different fonts
for different parts of a single piece of text. Here's a solution that
demonstrates this approach ...
pdfFonts(stdsym=Type1Font("standardsymbol",
c("Helvetica.afm",
"Helvetica-Bold.afm",
"s050000l.afm",
"Helvetica-BoldOblique.afm",
"Symbol.afm"),
encoding="CP1253"))
pdf("RquestionEncSym2.pdf")
set.seed(1)
Data=rnorm(100,sd=10000)
plot(density(Data))
text(25000,0.00003,
bquote(bold(italic("\u03c3") == .(mySigma)),
list('mySigma'=format(round(sd(Data),digits=3),
big.mark=","))),
family="stdsym", col="blue")
dev.off()
The new font family is slightly different in this example (the standard
symbol font is now in place of the italic font within the font family)
and the major difference is the use of plotmath to draw the text. In
particular, the sigma symbol is being drawn with an italic font face,
italic("\u03c3"), while the rest of the expression is bold. This means
that the digits remain bold while the sigma symbol comes from the
standard symbol font.
Only problem is, the symbol character is STILL not bold. But this
example has demonstrated the ideas we need to propose a final possible
solution.
4.
The extra step that we need, beyond the previous solution, is to make
use of a font that has a BOLD sigma symbol in it. The following code
gives an example, but this is based on fonts that are available on my
particular Linux box as part of the LaTeX installation; you may have to
change the specification of the new font to point to a font that you
have (which may require you to download/install a new font).
pdfFonts(BS=Type1Font("BoldSymbol",
c("Helvetica.afm",
"Helvetica-Bold.afm",
"/usr/share/texmf/fonts/afm/public/pl/plmib10.afm",
"Helvetica-BoldOblique.afm",
"Symbol.afm"),
encoding="CP1253"))
pdf(file="Rquestion.pdf")
set.seed(1)
Data=rnorm(100,sd=10000)
plot(density(Data))
text(25000,0.00003,
bquote(bold(italic("\u03c3") == .(mySigma)),
list('mySigma'=format(round(sd(Data),digits=3),
big.mark=","))),
family="BS", col="blue")
dev.off()
embedFonts("Rquestion.pdf",
fontpaths="/usr/share/texmf/fonts/type1/public/pl/")
The other difference in this example is the extra call to embedFonts()
at the end. This is necessary when using a font that your PDF viewer is
unlikely to know about. This step makes the special font part of the
PDF file, so the result should be able to be viewed anywhere.
Now, the quality of the final result will depend on which font you use
and how strong its bold symbols are. For me, the result is comparable
to what you get from Solution 1, so its questionable whether the extra
effort is worthwhile. But mucking around with this example found a bug
in R that I was able to fix, so all's not lost :)
Hope there is something in there that you can work with.
Paul
Thanks for the help,
Jonathan
----- Original Message ----- From: "Paul Murrell"
<p.murr...@auckland.ac.nz> To: "Jonathan R. Blaufuss"
<blauf...@carleton.edu> Cc: "Scott Sherrill-Mix"
<shesc...@mail.med.upenn.edu>, r-help@r-project.org Sent: Wednesday,
August 12, 2009 4:40:49 PM GMT -06:00 US/Canada Central Subject: Re:
[R] Using bold font with bquote
Hi
Jonathan R. Blaufuss wrote:
Scott, Your suggestion works great for changing the numbers to bold
font, but is it possible to change the sigma symbol and the equals
sign to bold font as well? I've poked around ?plotmath and am I
right in saying that there is a different method for controlling
symbol fonts?
R graphics only recognizes a plain symbol font (it has this weird
idea that a symbol font is a font face like bold or italic).
For your particular example, because it is not a complex math
formula, you might be able to do a workaround by constructing a
simple string and specifying the symbol that you want using Unicode.
Depending on what system and fonts you have, the following might work
...
text(25000,0.00004, paste("\u03c2 = ",
format(round(sd(Data),digits=3),big.mark=",")), font=2, col="blue")
Paul
Thank you for your help,
Jonathan
----- Original Message ----- From: "Scott Sherrill-Mix"
<shesc...@mail.med.upenn.edu> To: "Jonathan R. Blaufuss"
<blauf...@carleton.edu> Cc: r-help@r-project.org Sent: Wednesday,
August 12, 2009 12:43:12 PM GMT -06:00 US/Canada Central Subject:
Re: [R] Using bold font with bquote
From ?plotmath, it looks like when using expressions you set the
font
inside the expression (e.g. bold(x)). It looks you tried this
already but I wonder if there was something tiny out of place since
the following works for me:
text(25000,0.00003,bquote(bold(sigma==.(mySigma)),list('mySigma'=format(round(sd(Data),digits=3),big.mark=","))),
col='blue')
Scott
Scott Sherrill-Mix Department of Microbiology University of
Pennsylvania 402B Johnson Pavilion 3610 Hamilton Walk Philadelphia,
PA 19104-6076
On Wed, Aug 12, 2009 at 12:36 PM, Jonathan R.
Blaufuss<blauf...@carleton.edu> wrote:
I'm trying to annotate a density plot and I'm using bquote to
paste the sigma symbol next to the numeric text of the standard
deviation calculation that I am performing. I have been able to
successfully turn the sigma symbol and numeric output the color
blue, but when I try to change the font of the text to bold, R
doesn't seem to recognize the "font=" command in the same way
here as it does with "col=". (My code is below)
set.seed(1) Data=rnorm(100,sd=10000) plot(density(Data))
text(25000,0.00003, bquote(sigma==.(mySigma),
list('mySigma'=format(round(sd(Data),digits=3),big.mark=","))),
col="blue")
After searching the help files I've tried using the expression
command with "bold()" as well as inserting "font=2" after the
color command. However, I can't seem to get it to work.
Can someone please point me to a resource that will help me
figure this out?
Thank You,
Jonathan
______________________________________________
R-help@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.
______________________________________________ R-help@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.
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
p...@stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/
______________________________________________
R-help@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.
