Dear R Gurus,
I'm seeing some strange behavior that I can't explain. I'm
generating a figure for a paper and I like to save the script (no matter how
simple) for future reference. My practice is to write the script and run it
using the 'source()' function. What's weird is that the resultant
figure is not readable by OS X 10.7.0 (Lion). While trying to figure out what I
did wrong, I discovered that typing the exact same code into the R prompt
(running in Terminal) will produce the figure as I would expect it. The only
idea I have is that something has changed in Lion that doesn't allow
'source()' to interpret it properly.
Any ideas? Here is the exact code I'm using:
1 x<-read.delim("path/data.txt")
2
3
pdf("path/PaperFig-hist_of_perc_change-individ_samps-by_subtype.pdf")
4 histogram(~Total.Change,data=x,xlab="Percent Change")
5 dev.off()
I appreciate any help. I'm especially curious if there's a Lion user who
could give this a try.
OS X 10.7.0 (Lion)
R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
On 11-08-04 5:24 PM, Mark Ebbert wrote:> Dear R Gurus, > > I'm seeing some strange behavior that I can't explain. I'm generating a figure for a paper and I like to save the script (no matter how simple) for future reference. My practice is to write the script and run it using the 'source()' function. What's weird is that the resultant figure is not readable by OS X 10.7.0 (Lion). While trying to figure out what I did wrong, I discovered that typing the exact same code into the R prompt (running in Terminal) will produce the figure as I would expect it. The only idea I have is that something has changed in Lion that doesn't allow 'source()' to interpret it properly. > > Any ideas? Here is the exact code I'm using: > 1 x<-read.delim("path/data.txt") > 2 > 3 pdf("path/PaperFig-hist_of_perc_change-individ_samps-by_subtype.pdf") > 4 histogram(~Total.Change,data=x,xlab="Percent Change") > 5 dev.off() > > I appreciate any help. I'm especially curious if there's a Lion user who could give this a try.I don't have Lion, but it would be helpful to know what "not readable" means. If you try to open the file in Preview, what happens? Duncan Murdoch> > OS X 10.7.0 (Lion) > R version 2.13.0 (2011-04-13) > Copyright (C) 2011 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > ______________________________________________ > 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.
Save the result of histogram(), then print() the saved object.
On Aug 4, 2011 5:13 PM, "Mark Ebbert" <Mark.Ebbert@hci.utah.edu>
wrote:
Dear R Gurus,
I'm seeing some strange behavior that I can't explain. I'm
generating a
figure for a paper and I like to save the script (no matter how simple) for
future reference. My practice is to write the script and run it using the
'source()' function. What's weird is that the resultant figure is
not
readable by OS X 10.7.0 (Lion). While trying to figure out what I did wrong,
I discovered that typing the exact same code into the R prompt (running in
Terminal) will produce the figure as I would expect it. The only idea I have
is that something has changed in Lion that doesn't allow 'source()'
to
interpret it properly.
Any ideas? Here is the exact code I'm using:
1 x<-read.delim("path/data.txt")
2
3
pdf("path/PaperFig-hist_of_perc_change-individ_samps-by_subtype.pdf")
4 histogram(~Total.Change,data=x,xlab="Percent Change")
5 dev.off()
I appreciate any help. I'm especially curious if there's a Lion user who
could give this a try.
OS X 10.7.0 (Lion)
R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
______________________________________________
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.
[[alternative HTML version deleted]]
Note that ***histogram()*** (as opposed to "hist()") is a function
from the
"lattice" package. So at some stage you must have issued the command
"require(lattice)" or equivalently "library(lattice)". (So
your ``exact
code''
is a little misleading.)
You are thus getting bitten by the fact that the output of lattice
plot functions must be explicitly *printed* when called from within
a function such as source(). See fortune("line 800"). They
needn't
be explicitly printed when called from the command line, which is
why you are getting the figure you expect by typing the code at the
R prompt.
So put
print(histogram(~Total.Change,data=x,xlab="Percent Change"))
in the file that you are source()-ing and all will be in harmony in the
universe.
Nothing really to do either with source() or with OS X Lion.
cheers,
Rolf Turner
P. S. Apropos of nothing (but speaking of lions) everyone should read
``The Lion of Boaz-Jachin and Jachin-Boaz'' by Russell Hoban. :-)
R. T.
On 05/08/11 09:24, Mark Ebbert wrote:> Dear R Gurus,
>
> I'm seeing some strange behavior that I can't explain. I'm
generating a figure for a paper and I like to save the script (no matter how
simple) for future reference. My practice is to write the script and run it
using the 'source()' function. What's weird is that the resultant
figure is not readable by OS X 10.7.0 (Lion). While trying to figure out what I
did wrong, I discovered that typing the exact same code into the R prompt
(running in Terminal) will produce the figure as I would expect it. The only
idea I have is that something has changed in Lion that doesn't allow
'source()' to interpret it properly.
>
> Any ideas? Here is the exact code I'm using:
> 1 x<-read.delim("path/data.txt")
> 2
> 3
pdf("path/PaperFig-hist_of_perc_change-individ_samps-by_subtype.pdf")
> 4 histogram(~Total.Change,data=x,xlab="Percent Change")
> 5 dev.off()
>
> I appreciate any help. I'm especially curious if there's a Lion
user who could give this a try.
>
> OS X 10.7.0 (Lion)
> R version 2.13.0 (2011-04-13)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)