Re: publication quality graphs
[snip overview of Publication quality graphing packages] Jamie Rollins [EMAIL PROTECTED] writes: Thanks for the overview, Stuart. Very useful. Indeed it was. I would find this sort of comparison very useful on a web site. Perhaps it could be put on the wiki? Chris -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: publication quality graphs
Hi, On Fri, 14 Oct 2005, Stuart Prescott wrote: Hi again, thanks for your responses so far -- some interesting ideas I had a play with PyX some more yesterday and piped the data through the aspline utility (package: spline) to get an interpolated smooth curve. That worked quite nicely for me (using the python pipes object to stream in the data). I'm quite liking pyx as a concept, although I'm still not convinced that it's a sustainable approach in the long run. But I did realise that it's not particularly efficient to be trying to do this in python (which I will have to learn to use PyX) instead of perl (which I am quite comfortable in). Anyone know of a perl graphing module with the power of PyX? Learning python is not that hard. It takes about half a day to get (more than) the basics: See e.g. - for a quick 6 page start - instant python: http://www.hetland.org/python/instant-python.php - More is offered in the python tutorial http://docs.python.org/tut/tut.html And even more links of course on the docs page of python http://docs.python.org/tut/tut.html This one http://www.hackdiary.com/slides/lpw2004/ discusses python for perl programmers, maybe this helps as well. Personally I even think that you don't have to go through the above, but just learn while creating the graphics. PyX (http://pyx.sourceforge.net/) comes with *many* examples, see e.g. http://pyx.sourceforge.net/examples/graphs/index.html ranging from simple to very sophisticated. Especially, when the data are in files, you just have to do from pyx import * g = graph.graphxy(width=5) g.plot(graph.data.file(two_column_data.dat, x=1, y=2)) g.writeEPSfile(simple) And that's it ;-). The quality, accuracy, and the excellent (La)TeX embedding for the fonts makes it my number 1 choice for real publication quality graphs. (I used to use gnuplot for all my plots, but converted recently. For example all the plots in http://www.physik.tu-dresden.de/~baecker/pub21.html were generated with PyX). Also I should mention that the developers of PyX are very open to questions/suggestions (for example I forwarded the evaluation and they already started to think about the spline interpolation!). Let me bring in another one, matplotlib: http://matplotlib.sourceforge.net/ See the examples at http://matplotlib.sourceforge.net/screenshots.html It is also based on python and together with - ipython http://ipython.scipy.org/ - Numeric (soon to be superseeded by scipy core http://numeric.scipy.org/) - scipy http://www.scipy.org/ one gets an excellent framework for scientific computing in python (quite similar in many respects with matlab). Best, Arnd -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: publication quality graphs
Hi, I am a long-time Matlab user that is trying to migrate to Octave but have been having some issues with plotting. Octave by default uses gnuplot, which I think produces very satisfactory plots, but with which I have been having quite a bit of trouble exporting the plots to useful files. Octave also has support for plplot (which I noticed was not on your list), but I have no experience with it. I am using plplot and pgplot from perl/pdl which both are working nice, there is not much difference in the number of possible functions; for publications I am using gnuplot since I want to insert my graphs as tex-files, which can be done from gnuplot very easily. Do people have any suggestions for producing nice plots from Octave? Has anyone figured out a good way to print gnuplot plots produced with Octave? What about peoples experience with plplot? Thanks in advance for any advice. There is the eps-toolkit (debian package is called octave-epstk), which produces very nice eps-plots from octave, Andreas -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: publication quality graphs
why not using gnuplot + metapost You just have to select the metapost terminal and all the text will be generated from tex or Latex. so you can add equation etc.. I have done all my PhD thesis figures with this and the result was terrific :) bye frédéric -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: publication quality graphs
Thanks for the overview, Stuart. Very useful. However, I am not having any luck finding many of the packages you mention in etch; xmggrace, qtiplot, and pyx in particular don't turn up on a cursory search of packages in etch. Are they maybe included in packages under different names? I am a long-time Matlab user that is trying to migrate to Octave but have been having some issues with plotting. Octave by default uses gnuplot, which I think produces very satisfactory plots, but with which I have been having quite a bit of trouble exporting the plots to useful files. Octave also has support for plplot (which I noticed was not on your list), but I have no experience with it. Do people have any suggestions for producing nice plots from Octave? Has anyone figured out a good way to print gnuplot plots produced with Octave? What about peoples experience with plplot? Thanks in advance for any advice. jamie. On Thu, Oct 13, 2005 at 01:57:38PM +1000, Stuart Prescott wrote: Hi all, A question that has come up a few times on this list is how people go about producing publication quality graphs. I'm revisiting this question as I'm yet to find a method that actually works for me. Part of this is that I am used to doing things in a particular way (which might have to change!) and part of this is shortcomings in various packages that I've tried. After a day or so of frustration with any given app, I end up going back to Origin (Origin6 under WINE mostly works). Here, I'd like to describe how I normally plot data and why the various apps that I've tried don't work for me (below). Hopefully, this will incite some discussion and regular users of these apps can suggest some add-ons or simple changes to my workflow that will turn them from being a pain in the backside to being a useful utility. Or perhaps this will encourage someone (me?) to hack at these apps until they become more useful to people like me. All comments welcome! cheers Stuart * current workflow using Origin I normally have data from a number of different (but related) experiments in the one file (perhaps X1 Y1 X2 Y2 or X Y1 Y2 Y3) format that has been exported from OOo.calc or excel or perhaps from a data analysis program that I have written for the purpose. The files are usually tab-delimited and I can just Import ASCII in Origin and all is well. It sets the column names to be the headers from the text file. I can then create plots with some or all of the data and will frequently want to add new data to a plot from another worksheet trivially etc. In the end I produce an EPS graphic for use in LaTeX or a PNG graphic for MSWord/MSPowerpoint. I like the project paradigm of Origin where data, settings and graphs are all together allowing you to add new data to plots, plot things in different ways etc. I don't just make the one final publication quality graph in an Origin project; rather, I usually have several different publication graphs in the one project (and often both print and presentation versions of these graphs too) as well as other graphs made while I explore the data. I tend not to use Origin for data manipulation as it is much more cumbersome than using a proper spreadsheet program like excel or OOo calc. * OOo calc Ha. Nice thought. Produces graphs that look as bad as M$Excel but can't even handle X1 Y1 X2 Y2 data (only X Y1 Y2). Non-starter even for just having a quick look at data, even if it does meet the project paradigm. * xmggrace It can't read in any of my data files. Bit of a showstopper, really I almost always have data with columns: X Y1 Y2 Y3... or X1 Y1 X2 Y2 X3 Y3... and I *always* have text column headings labelling the data. It chokes on this sort of thing and I'm not going to manually import hundreds of individual files (or columns piped through tail +1 | cut -f etc) through that tedious import dialogue. * qtiplot In a file with X1 Y1 X2 Y2 etc where the data streams are different lengths, it chokes... all the data is left-aligned in the import (i.e. if X1 Y1 has 20 rows but X2 Y2 has 30 rows, X1 Y1 will gain an extra 10 rows of data at the expense of X2 Y2). It also doesn't permit you to define multiple X columns per data sheet or edit an existing plot to change which column is to be used for the X or Y data etc (which is useful in transferring settings from one plot to another in the absence of styles or templates). Finally, the plots don't scale to the size of the window (there is no defined page size) so if you make the window bigger, then you have to manually increase all the font sizes yourself. * labplot Shares many of the same bugs/problems as qtiplot. But you also can't add a new curve to an existing graph unless you read it in from a data file directly or it is a mathematical function (i.e. you can't use data already in a data sheet). Column headers are also discarded so you'd have to go back and relabel all
Re: publication quality graphs
On 10/13/05, Jamie Rollins [EMAIL PROTECTED] wrote: Thanks for the overview, Stuart. Very useful. However, I am not having any luck finding many of the packages you mention in etch; xmggrace, qtiplot, and pyx in particular don't turn up on a cursory search of packages in etch. Are they maybe included in packages under different names? xmgrace is in the package called grace. Do people have any suggestions for producing nice plots from Octave? Has anyone figured out a good way to print gnuplot plots produced with Octave? What about peoples experience with plplot? Thanks in advance for any advice. I've found the only usable solution for publication quality graphs to be the grace interface from octave-forge. It doesn't do 3D-plots though. Teemu
Re: publication quality graphs
Jamie Rollins wrote: Thanks for the overview, Stuart. Very useful. However, I am not having any luck finding many of the packages you mention in etch; xmggrace, qtiplot, and pyx in particular don't turn up on a cursory search of packages in etch. Are they maybe included in packages under different names? xmgrace is in package 'grace' or 'grace6', the latter being a development snapshot of a version 6 prerelease, that I mentioned on another thread that I prefer, if I'm not bothered about keeping the data around (the file format isn't stabilised yet, afaict). -- Neil -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: publication quality graphs
Hi again, thanks for your responses so far -- some interesting ideas I had a play with PyX some more yesterday and piped the data through the aspline utility (package: spline) to get an interpolated smooth curve. That worked quite nicely for me (using the python pipes object to stream in the data). I'm quite liking pyx as a concept, although I'm still not convinced that it's a sustainable approach in the long run. But I did realise that it's not particularly efficient to be trying to do this in python (which I will have to learn to use PyX) instead of perl (which I am quite comfortable in). Anyone know of a perl graphing module with the power of PyX? Jamie, I can't help you with octave questions, but I can help with the others: * xmgrace my typo: s/xmggrace/xmgrace/ sorry. As already noted, it's in the package grace6 (or grace, diff versions etc) as it is a rewrite of an older program called xmgr * qtiplot has no debian package available (for free at least). Source is available from http://soft.proindependent.com/qtiplot.html It has a few dependencies, you'll also need to compile qwtplot3d yourself, the rest are in Debian. * pyx pyx is a python package so the package is called python-pyx Finally, Neil Pilgrim wrote: * OOo calc Maybe this will improve in the upcoming version 2? If only. Despite many many requests for this feature, it's only just got a target milestone... OOo3.0 so don't hold your breath. http://qa.openoffice.org/issues/show_bug.cgi?id=3997 cheers Stuart -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: publication quality graphs
Hi Stuart,
On Thu, 2005-10-13 at 13:57 +1000, Stuart Prescott wrote:
* current workflow using Origin
I normally have data from a number of different (but related)
experiments in the one file (perhaps X1 Y1 X2 Y2 or X Y1 Y2 Y3) format
that has been exported from OOo.calc or excel or perhaps from a data
analysis program that I have written for the purpose. The files are
usually tab-delimited and I can just Import ASCII in Origin and all is
well. It sets the column names to be the headers from the text file. I
can then create plots with some or all of the data and will frequently
want to add new data to a plot from another worksheet trivially etc. In
the end I produce an EPS graphic for use in LaTeX or a PNG graphic for
MSWord/MSPowerpoint. I like the project paradigm of Origin where data,
settings and graphs are all together allowing you to add new data to
plots, plot things in different ways etc. I don't just make the one
final publication quality graph in an Origin project; rather, I usually
have several different publication graphs in the one project (and often
both print and presentation versions of these graphs too) as well as
other graphs made while I explore the data. I tend not to use Origin for
data manipulation as it is much more cumbersome than using a proper
spreadsheet program like excel or OOo calc.
So, you're essentially making plots of pairs of data, or the like?
* gnuplot
I'll confess that I have a deep seated aversion to gnuplot that dates
back to my undergraduate days which is probably unfair. Having said
that, I do prefer to be able to manipulate the graphs in real time *and*
be able to save the settings and data as a project. With gnuplot you can
do one or other (either run it from a script which is pretending to be a
project file or some sort, or you can do it in real time.)
My initial suggestion would be this, but I can understand were you're
coming from. I have students that would sympathise with you on this
one :-)
* others?
Are there any other utils that you can suggest that might meet my
requirements? I'm happy to try things out and will post back reviews of
them too when I have a chance.
ROOT :-) OK, I know that this suggestion was a given coming from me.
However, in particle, nuclear, and heavy ion Physics we've been using
PAW (Debian package paw) from CERN for many years now. It's old,
written in Fortran 66 (yes, not Fortran 77, 90, 95 or any of that modern
stuff - good old Fortran :-), and the interface isn't exactly that easy
to deal with.
The successor of PAW is ROOT (and much more than that too). ROOT is
essentially a set of C++ classes for doing various things related to
data analysis, storage, GRID (the buzz-word), and so on. It's used
extensively to prepare all sorts of plots, ranging from the casual plot
to impress your supervisor to plot that are put in articles and books.
There's a interpreter interface that's useful for plotting stuff, as
well as some GUI tools. The scripting language is C++. So, suppose
you have a datafile like
# X Y EX EY
0.1 0.000815046 0.0127950.028549
0.2 0.00882257 0.0095365 0.0939285
0.3 0.0367130.0481904 0.191606
0.4 0.0596013 0.0191006 0.244134
0.5 0.1761940.0305726 0.419755
then you could plot this in ROOT with the following script
void
plotit(const char* fname)
{
ifstream file(fname);
TGraphErrors* g = new TGraphErrors;
g-SetMarkerStyle(20);
int i = 0;
while (true) {
char c = file.peek();
if (c == '#') {
string s;
getline(file,s);
continue;
}
double x, y, ex, ey;
file x y ex ey;
if (file.eof()) break;
g-SetPoint(i, x, y);
g-SetPointError(i, ex, ey);
}
file.close();
g-Draw(acp);
}
To plot the data in `data.dat', do
root
Root .x plotit.C(data.dat)
Titles and the like can be changed either in he script, or interactively
via the GUI. It's also possible to define preset `styles' e.g., a style
for print, a style for presentations, and so on.Histograms are
easily made too, and there's a special storage format called Tree's that
has many automatic features.
You can get the ROOT packages by adding
deb http://mirror.phy.bnl.gov/debian-root unstable root
to your sources.list (see also thread on ROOT in this mailing list).
** conclusions
The two main things that I can condense out of this are that:
* there is nothing in linux land that even comes close to Origin for
flexible scientific graphing and data management. That's a pity... linux
leads in everything else, but I know very few other people who will
Re: publication quality graphs
Hi all, I would just like to throw out PGPLOT. According to the website, http://www.astro.caltech.edu/~tjp/pgplot/ : The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. In my lab some of us use it to make pubilcation quality plots (my advisor considers the quality to be superior to gnuplot, for what it's worth). We also use it as a part of our data collection (because it is Fortran or C library) programs to visualize our experiments in real time (no Labview here). Anyway, I don't use it too much unless I need really good quality plots because you have to make (and compile) a Fortran program to use it. But, I do think it is worth considering. -Jordan Mantha -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
publication quality graphs
Hi all, A question that has come up a few times on this list is how people go about producing publication quality graphs. I'm revisiting this question as I'm yet to find a method that actually works for me. Part of this is that I am used to doing things in a particular way (which might have to change!) and part of this is shortcomings in various packages that I've tried. After a day or so of frustration with any given app, I end up going back to Origin (Origin6 under WINE mostly works). Here, I'd like to describe how I normally plot data and why the various apps that I've tried don't work for me (below). Hopefully, this will incite some discussion and regular users of these apps can suggest some add-ons or simple changes to my workflow that will turn them from being a pain in the backside to being a useful utility. Or perhaps this will encourage someone (me?) to hack at these apps until they become more useful to people like me. All comments welcome! cheers Stuart * current workflow using Origin I normally have data from a number of different (but related) experiments in the one file (perhaps X1 Y1 X2 Y2 or X Y1 Y2 Y3) format that has been exported from OOo.calc or excel or perhaps from a data analysis program that I have written for the purpose. The files are usually tab-delimited and I can just Import ASCII in Origin and all is well. It sets the column names to be the headers from the text file. I can then create plots with some or all of the data and will frequently want to add new data to a plot from another worksheet trivially etc. In the end I produce an EPS graphic for use in LaTeX or a PNG graphic for MSWord/MSPowerpoint. I like the project paradigm of Origin where data, settings and graphs are all together allowing you to add new data to plots, plot things in different ways etc. I don't just make the one final publication quality graph in an Origin project; rather, I usually have several different publication graphs in the one project (and often both print and presentation versions of these graphs too) as well as other graphs made while I explore the data. I tend not to use Origin for data manipulation as it is much more cumbersome than using a proper spreadsheet program like excel or OOo calc. * OOo calc Ha. Nice thought. Produces graphs that look as bad as M$Excel but can't even handle X1 Y1 X2 Y2 data (only X Y1 Y2). Non-starter even for just having a quick look at data, even if it does meet the project paradigm. * xmggrace It can't read in any of my data files. Bit of a showstopper, really I almost always have data with columns: X Y1 Y2 Y3... or X1 Y1 X2 Y2 X3 Y3... and I *always* have text column headings labelling the data. It chokes on this sort of thing and I'm not going to manually import hundreds of individual files (or columns piped through tail +1 | cut -f etc) through that tedious import dialogue. * qtiplot In a file with X1 Y1 X2 Y2 etc where the data streams are different lengths, it chokes... all the data is left-aligned in the import (i.e. if X1 Y1 has 20 rows but X2 Y2 has 30 rows, X1 Y1 will gain an extra 10 rows of data at the expense of X2 Y2). It also doesn't permit you to define multiple X columns per data sheet or edit an existing plot to change which column is to be used for the X or Y data etc (which is useful in transferring settings from one plot to another in the absence of styles or templates). Finally, the plots don't scale to the size of the window (there is no defined page size) so if you make the window bigger, then you have to manually increase all the font sizes yourself. * labplot Shares many of the same bugs/problems as qtiplot. But you also can't add a new curve to an existing graph unless you read it in from a data file directly or it is a mathematical function (i.e. you can't use data already in a data sheet). Column headers are also discarded so you'd have to go back and relabel all the columns. (OK, on the 1 week time scale you can just remember them, but on the 1 year timescale you need them labelled, and I always assume that i'm going to have to come back to it on that timescale as it can be that long between doing the work and publishing it.) It also can't generate smooth curves (e.g. splines) between data points. * scigraphica Importing X1 Y1 X2 Y2 data into a sheet causes the data to be truncated at the number of rows in X1. Column headers are imported, but if more than one column has the same name then only the left-most column is used when you come to graph that dataset. * gnuplot I'll confess that I have a deep seated aversion to gnuplot that dates back to my undergraduate days which is probably unfair. Having said that, I do prefer to be able to manipulate the graphs in real time *and* be able to save the settings and data as a project. With gnuplot you can do one or other (either run it from a script which is pretending to be a project file or some sort, or you can do it in real time.) *gri Works great for me for quick
Re: publication quality graphs
On Thu, Oct 13, 2005 at 01:57:38PM +1000, Stuart Prescott wrote: Hi all, A question that has come up a few times on this list is how people go about producing publication quality graphs. I'm revisiting this question as I'm yet to find a method that actually works for me. Part of this is that I am used to doing things in a particular way (which might have to change!) and part of this is shortcomings in various packages that I've tried. After a day or so of frustration with any given app, I end up going back to Origin (Origin6 under WINE mostly works). Here, I'd like to describe how I normally plot data and why the various apps that I've tried don't work for me (below). I've also had tried several alternatives trying to find the 'right' tool. In my Windows days I used Matlab, but never used it for the final publication graph. I rather took the data and imported the data into Axum, whose graphs looked much better to me. I tried Origin, but never really liked it. Too graphical for my tastes :-) And for me, contrary to you, this project concept has always confused me. For me the problem is: raw data - eps graph. Currently I don't do 3d graphs, so xmgrace is just fine for me, and has the kind of configurability I need. But I don't like to repeat settings, so what I did is to write a C++ code which takes the data and outputs a file in the format .agr used by grace. Then I use the gracebat command to convert to eps. Actually, the C++ code takes as input a script file, reading data and graphic settings, and all the work is called from a single command line. I feel I am doing the same as Gri in a way, but, like you, I tried it and loved the idea, but the graphs are not quite what I want, and couldn't configure the bits I needed. :-( Regards, Victor -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: publication quality graphs
On Thu, 13 Oct 2005, Stuart Prescott wrote: A question that has come up a few times on this list is how people go about producing publication quality graphs. I'm revisiting this question as I'm yet to find a method that actually works for me. I personally use R here for almost all of the publication quality graphs that I need to make here. My basic workflow looks like the following: 1) data entry into gnumeric 2) export to tab delineated files 3) tweak .R file so that it does what I want it to do for this particular dataset [I've got a set of these that I use for different experiments/graph types that I use often.] 4) R --no-save foo.R; to run the R file 5) ps2pdf if I need to send it to people who don't have gv [I actually have makefiles to do 45] Of course, R is probably a bit more difficult to get started in, but the power of the language makes it quite useful to me, despite its steep learning curve. http://rzlab.ucr.edu/debian/debian-science/ should give you sort of an idea of what I'm doing. [Ignore the gigantic +/-, that was a less than stellar experiment.] Don Armstrong -- I never until now realized that the primary job of any emoticon is to say excuse me, that didn't make any sense. ;-P -- Cory Doctorow http://www.donarmstrong.com http://rzlab.ucr.edu -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
