Publication-quality graphing program

[radek42]

Hi,

I am slowly making move to mac, but I still have some worries. As I am preparing to migrate my main work computer (physics research) I am trying to identify replacement software for my graphing needs.

I need to be able to produce 2d and 3d, publication-quality plots for posters and paper publications (something similar to Origin). Since I am using Linux over past couple of years I got more-less used to gnuplot which works well, but it's not too user friendly (no GUI). I would prefer open-source, gpl-licence, cross-platform software if at all possible (for easy sharing with colleagues who mostly use Wins).

I'd like to hear your experience with various pieces of software as well as transition from Win/Linux to OSX.

Thanks, Radek

----- edit -----
I'd prefer to avoid Fink since it needs massive XCode installed and I plan to run it on MBA. Is there a way to install gnuplot only?

 

[miles01110]

I would prefer open-source, gpl-licence, cross-platform software if at all possible (for easy sharing with colleagues who mostly use Wins).

root or Matlab.

 

[radek42]

Thanks for the response. I never thought of Matlab as a graphing program ... I suppose it can do graphs, but so can Excel ... and it is ... disaster to say the least.

Root reminds me gnuplot a bit. I actually considered gnuplot since I used it in Linux for couple years. I could do pretty much what I needed (not perhaps what I wanted), but I noticed you loose touch quickly if you don't use it on fairly regularly which I did not. Plus, installing on mac seems a pain at least compared to Linux where it was a part of standard repository.

I was used to Origin back in my Win days, but that's many years ago. I don't want virtual machine so that is out of the question. After some more research I am considering:

1. KaleidaGraph ... decent feature-set; cheap
2. DeltaGraph ...... perhaps a bit more; more expensive
3. IgorPro ........... "everything" think Cadillac; pretty expensive

4. QtiPlot ............ seems decent; free
I'd really would like it, but again, it seems a pain to install unless you pay and get binaries. I also tried it in the past under Linux and it was unstable to the point of being unusable. That being said, I have a bit reservation towards it right now. Esp. considering I picked mac for simplicity; less fuss, more work

I'd appreciate if people could comment on these application, preferably if you use more that one for some time. Do you still use both or all three? If not, what made you switch? Also, did you find in either program anything that you could not do?

Of course, if you have other suggestions I welcome those as well.

Thanks, R>

PS; I perhaps should say I'll be using it in science/research field so I am looking at educational versions.

----- Added -----

I just came across "plot" which looks nice and comes as universal binary .... Did anybody use it? R>

----- Added again -----

Now I remember why I did not downloaded already ... last update was 2007 ... that's no go! R>

root or Matlab.

 

[mobilehaathi]

You can get gnuplot for osx by using MacPorts. Also consider R, octave, or sage!

Edit: just saw you prefer not to use Fink, which is quite similar to MacPorts. So I guess that option is out?

 

[radek42]

Thanks. I'll look into ones you suggested.

It's not I am against Macports/Fink, but I am running on MBA w/ SSD. Therefore I wanted to avoid downloading and installing Xcode for that purpose only. I might need fortran/C/C++ but I will see ... that might be for a different thread

R: looks interesting.

Octave: again as Matlab, I think of it as computation tool (like Mathematica, Maple, etc)

Thanks for input .... keep them coming!

R>

You can get gnuplot for osx by using MacPorts. Also consider R, octave, or sage!

Edit: just saw you prefer not to use Fink, which is quite similar to MacPorts. So I guess that option is out?

 

[mobilehaathi]

Thanks. I'll look into ones you suggested.

It's not I am against Macports/Fink, but I am running on MBA w/ SSD. Therefore I wanted to avoid downloading and installing Xcode for that purpose only. I might need fortran/C/C++ but I will see ... that might be for a different thread

R: looks interesting.

Octave: again as Matlab, I think of it as computation tool (like Mathematica, Maple, etc)

Thanks for input .... keep them coming!

R>

Indeed, R, sage, and octave are all computational tools, but they work reasonably well for figure generation too. In particular, I use R for all of my plotting and basic statistics needs. It can be a major pain in many respects, but it gives exquisite control over figure creation and can export directly to .eps format. Plus it is GNU and richly supported by the community.

 

[klaxamazoo]

I use Datagraph and really like it.
http://www.visualdatatools.com/DataGraph/

It is only does 2D plots and only runs on OS X, but the plots are extremely easy to make and look great. Visual Data Tools also makes a 3D plotting program called DataTank, but I haven't used it.

Also, the Datagraph and DataTank frameworks are available and can be readily incorporated into your own programs. I got tired of Matlab's license restrictions and found that writing my analysis programs in C/Objective-C to be easier and have a lot more features than my old Matlab scripts.

I've also tried Plot, but I found it hard to use and I don't think the developer is still working on it. The plots look pretty good, but I never liked the workflow.


On a related note, some other scientific software worth looking into include:
Papers: www.mekentosj.com - a journal organizer/finder
LyX - a LaTeX wrapper
SugarSync - keep your computers synced and have an offsite backup of your data

 

[mobilehaathi]

It just occurred to me that when I worked in an astrophysics lab (a long time ago) we used IDL. It isn't Free, but they do have student licenses available.

 

[radek42]

Quick update (in case anybody cares

So far I have tried DataGraph and Kaleidagraph. Both are pretty good, but not without glitches (it might be demo version tho). For instance, I cannot set fixed range in DataGraph ... so simple, but I just could not find it. Still not sure which one I'd pick.

Igor Pro just finished downloading so I am gonna try that as well as DeltaGraph ...

I have checked IDL's web site, but I could not find pricing without login ... strange.

Anyway, thanks everybody for great suggestions ... keep 'em coming.

R>

 

[radek42]

Thanks for comments.

As I mentioned earlier I find DataGraph a bit awkward, but I only spent about hour with it. I could managed everything I wanted .. eventually. I do not like the layout.

Igor was also good, but it's pricy.

Thanks for other suggestions as well. Somebody already mentioned papers to me. It looks interesting, but BibDesk seems pretty capable as well with very similar functionality. As for LateX editor I'll stick with texshop for now. Btw, did you go with full mactex install or basictex .... I went with formal, but I am thinking that basictex might be enough since I just need latex, bibtex, revtex and graphics packages. Pretty standard I'd say and it might save some precious disk space

Back on the topic: I'm leaning towards Igor, but DataGraph might do the job as well. I would miss 3D graphs occasionally too.

I'll see.

Cheers, R>

I use Datagraph and really like it.
http://www.visualdatatools.com/DataGraph/

It is only does 2D plots and only runs on OS X, but the plots are extremely easy to make and look great. Visual Data Tools also makes a 3D plotting program called DataTank, but I haven't used it.

Also, the Datagraph and DataTank frameworks are available and can be readily incorporated into your own programs. I got tired of Matlab's license restrictions and found that writing my analysis programs in C/Objective-C to be easier and have a lot more features than my old Matlab scripts.

I've also tried Plot, but I found it hard to use and I don't think the developer is still working on it. The plots look pretty good, but I never liked the workflow.


On a related note, some other scientific software worth looking into include:
Papers: www.mekentosj.com - a journal organizer/finder
LyX - a LaTeX wrapper
SugarSync - keep your computers synced and have an offsite backup of your data

 

[klaxamazoo]

Thanks for comments.

As I mentioned earlier I find DataGraph a bit awkward, but I only spent about hour with it. I could managed everything I wanted .. eventually. I do not like the layout.

Igor was also good, but it's pricy.

Thanks for other suggestions as well. Somebody already mentioned papers to me. It looks interesting, but BibDesk seems pretty capable as well with very similar functionality. As for LateX editor I'll stick with texshop for now. Btw, did you go with full mactex install or basictex .... I went with formal, but I am thinking that basictex might be enough since I just need latex, bibtex, revtex and graphics packages. Pretty standard I'd say and it might save some precious disk space

Back on the topic: I'm leaning towards Igor, but DataGraph might do the job as well. I would miss 3D graphs occasionally too.

I'll see.

Cheers, R>

I installed the full LaTeX package and used LyX as a WYSIWYM wrapper, which lets me focus on my writing instead of looking at a bunch of mark-up code. I don't have any experience with the smaller install.

I would recommend giving Papers another chance. Its ability to search multiple sources (i.e. Google Scholar, Web of Science, etc.) at the same time and route through your library proxy so that you can automatically download the .pdf into the program is nice.

More importantly, it scrubs the webpage for all the citation information (i.e. page numbers, volume, number, etc.) so that you don't have to spend time copy-pasting into BibDesk or some other program.

Datagraph does have a different way of doing things. I tried an Igor demo briefly but I didn't bother spending much time with it as I already had Datagraph.

To answer your concern on Fixed Range in Datagraph. Expand the Axis settings and update the "Restrict x:" or "Restrict y:" textFields. That will change the axis. You can also crop values in the data itself by expanding the Plot settings if you need to.

 

[Odd]

Did you consider Grapher?

Bundled with OS X, in the Utilities folder.
Clean graphs, does math, imports point sets. Even does animations.

 

[radek42]

I installed the full LaTeX package and used LyX as a WYSIWYM wrapper, which lets me focus on my writing instead of looking at a bunch of mark-up code. I don't have any experience with the smaller install.

I don't mind the markup part. I am quite used to it and I am faster typing in commands rather than clicking around, but that's personal preference.

I would recommend giving Papers another chance. Its ability to search multiple sources (i.e. Google Scholar, Web of Science, etc.) at the same time and route through your library proxy so that you can automatically download the .pdf into the program is nice.

More importantly, it scrubs the webpage for all the citation information (i.e. page numbers, volume, number, etc.) so that you don't have to spend time copy-pasting into BibDesk or some other program.

I believe Bibdesk now can do pretty much the same thing. Once I get used to it a bit I'll give Papers a try (if there is trial version).

Datagraph does have a different way of doing things. I tried an Igor demo briefly but I didn't bother spending much time with it as I already had Datagraph.

To answer your concern on Fixed Range in Datagraph. Expand the Axis settings and update the "Restrict x:" or "Restrict y:" textFields. That will change the axis. You can also crop values in the data itself by expanding the Plot settings if you need to.

I'll check when I get home.

I am looking at "R" again. It seems to have some sort of GUI some one can get going without remembering too many line commands.

Interestingly, I talked to other guy in our group what he is using to make plots on Mac ... as we talked I realized that Latex is full of commands to format text, tables, and images and I do not mind that too much. So perhaps apps like R, gnuplot, or root are back in the mix

I'll post back once I figure out how to install and run R ...

R>

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Bundled with OS X, in the Utilities folder.
Clean graphs, does math, imports point sets. Even does animations.

Interesting ... I guess sometimes the most obvious isn't that obvious. I could make it work, but I did not (in 5 mins or so) figure out how the plot different columns from the spreadsheet. I am sure it's doable.

I find one strange flaw/bug (are these even possible on mac? :
I wanted to move axis labels and number outside of the axis. I found the slider which moved text, but it only reached middle of axis and went back inside; almost like there is a wrong sign (or rather something like absolute value). I think it was the same for both x and y.

Has anybody else seen this?

R>

 

[mobilehaathi]

R is all CLI: even in the GUI all of your work will be typing commands.

 

[balamw]

I'd prefer to avoid Fink since it needs massive XCode installed and I plan to run it on MBA. Is there a way to install gnuplot only?

IIRC you can use fink/MacPorts with gcc/clang instead of the full Xcode:

A coupe of sources.

https://github.com/kennethreitz/osx-gcc-installer
http://hpc.sourceforge.net/

I have one of those on my MBA for MacPorts. I forget which.

B

 

[radek42]

R is all CLI: even in the GUI all of your work will be typing commands.

I just installed it on my old linux box (debian) soon to be replaced by MBA. You can do a bit using GUI, but mostly typing commands .... oh well.

It seems one can install gnuplot without XCode ... I downloaded couple packages last night, but I did not have a chance to try it .... I'll write back once I know more.

Thanks for posting. R>

----------

IIRC you can use fink/MacPorts with gcc/clang instead of the full Xcode:

A coupe of sources.

https://github.com/kennethreitz/osx-gcc-installer
http://hpc.sourceforge.net/

I have one of those on my MBA for MacPorts. I forget which.

B

Thanks. That would be great. I remember seeing notes about it somewhere ...

I definitely saw a note about HPC gcc compiler on R website ... apparently it does not play well with R.

Do you know if one can add fortran compiler to github? (something along these lines:
http://r.research.att.com/tools/
see GNU fortran compiler at the top).

This is great! Thanks. R>

 

[mobilehaathi]

I just installed it on my old linux box (debian) soon to be replaced by MBA. You can do a bit using GUI, but mostly typing commands .... oh well.

It seems one can install gnuplot without XCode ... I downloaded couple packages last night, but I did not have a chance to try it .... I'll write back once I know more.

Thanks for posting. R>

Didn't think you'd be against a CLI since you were using gnuplot.

Does gnuplot have a GUI?

 

[radek42]

Didn't think you'd be against a CLI since you were using gnuplot.

Does gnuplot have a GUI?

No, gnuplot does not have a gui.

As I said in my very first post; gnuplot was good even insanely awesome when scripted to plot my data files with a single click in thunar/nautilus. But in day-to-day work I found it awkward since I remember only half of commands I needed. By the time I learnt the commands I was done with my graphs ... until I needed to work on them weeks later remembering pretty much nothing again

If you don't use it, you loose it.

On the other hand I remember most of my latex stuff even after years. I'll see. I'll give R and gnuplot shot and see. I was hoping for some compatibility with my Wins coworkers (... and please don't say that gnuplot works in cygwin . That of course limits my options ... however, it is not a strict requirement.

Since I'd like to have fortran on my system perhaps hithub(gcc) + fotran (if possible) + gnuplot would work nicely. I will always have excel just to share graphs with others.

Any further suggestions / comments are still welcome

R>

 

[mobilehaathi]

I'll give R and gnuplot shot and see. I was hoping for some compatibility with my Wins coworkers (... and please don't say that gnuplot works in cygwin . That of course limits my options ... however, it is not a strict requirement.

Well, R is available for Windows too!

 

[radek42]

gcc w/o XCode

I was looking into github and I found this post:
http://kennethreitz.com/xcode-gcc-and-homebrew.html

You can now download CLI tools instead of complete IDE aka XCode (~170MB instead of 1.8GB!). I hope it'll work with fink/macport, gnuplot, fortran (see link couple posts up) and other stuff.

R>

 

[mobilehaathi]

I was looking into github and I found this post:
http://kennethreitz.com/xcode-gcc-and-homebrew.html

You can now download CLI tools instead of complete IDE aka XCode (~170MB instead of 1.8GB!). I hope it'll work with fink/macport, gnuplot, fortran (see link couple posts up) and other stuff.

R>

Hmmm, nice find. I knew you could install the CLI tools through XCode, but didn't realize it was also offered as a separate download.

 

[balamw]

You can now download CLI tools instead of complete IDE aka XCode (~170MB instead of 1.8GB!). I hope it'll work with fink/macport, gnuplot, fortran (see link couple posts up) and other stuff.

That was the point of my earlier post. I gave you two sources for a full pre-compiled CLI based development environment.

In order to support fortran on the github hosted version of gcc/clang, you'll probably need to follow the directions on building a package yourself from source.

On at least one box around here I have both Xcode and the hpc version of fortran, so that's always another option.

----------

Well, R is available for Windows too!

gnuplot used to be available as a native Win32 binary, current versions seem only to be built against Cygwin and MinGW.

I went between the Windows and Linux versions for my thesis work many moons ago.

B

 

[MisterMe]

....

I was used to Origin back in my Win days, but that's many years ago. I don't want virtual machine so that is out of the question. After some more research I am considering:

1. KaleidaGraph ... decent feature-set; cheap
2. DeltaGraph ...... perhaps a bit more; more expensive
3. IgorPro ........... "everything" think Cadillac; pretty expensive

4. QtiPlot ............ seems decent; free
I'd really would like it, but again, it seems a pain to install unless you pay and get binaries. I also tried it in the past under Linux and it was unstable to the point of being unusable. That being said, I have a bit reservation towards it right now. Esp. considering I picked mac for simplicity; less fuss, more work

I'd appreciate if people could comment on these application, preferably if you use more that one for some time. Do you still use both or all three? If not, what made you switch? Also, did you find in either program anything that you could not do?

Of course, if you have other suggestions I welcome those as well.

...

Origin is an application for Windows users who have much more money than brains. It is much more expensive than any of the Mac options that you named. However, you will be hard pressed to produce a nicer or more professional graph or to perform more in-depth analysis using Origin than using any of the less expensive options.

gnuplot is a CLI application that is used as the graphing engine of other applications. In that role it is fantastic. However, it is not 1993 anymore. You do not need to sacrifice ease-of-use for textbook-quality graphs. If you were a Mac user in 1993, you didn't need it then.

Now for your three options:

1. KaleidaGraph—Hews to the interface paradigm pioneered by the venerable graphing application Cricket Graph. In my not so humble opinion, Cricket Graph's UI was the best UI for a graphing program. In addition to its intuitive UI, KG sports 95% of the power of the most powerful application listed here. This is my primary graphing application.
2. DeltaGraph—During its early days, this application was targeted toward Excel users who needed to produce quality graphs for publication and presentation. There is probably no application available on any platform that can produce prettier graphs. Aesthetics aside, DeltaGraph is comparable in power to KaleidaGraph in its ability to analyze data and to produce science and engineering graphs.
3. IgorPro—I have used this application for decades and have recommended it to others. It is an acquired taste. IgorPro relies on keyboard commands and scripts to perform its work. Its GUI generates scripts that can be edited and extended at will. The scripting language is powerful and easy to use. But, the graphs.... The graphs! IgorPro has a print engine that produces technical graphs as fine as any application anywhere. The demonstrations produce graphs that replicate the pages from technical reference books.
4. QtiPlot—A Qt frameworks-based clone of Origin. Meh. Well, it is free.

Additional applications:

pro Fit—From Swiss developer Quantum Soft, this application features a powerful Pascal-like scripting language.

OmniGraphSketcher—From storied NeXTstep/MacOS X developer OmniGroup, this inexpensive application gives every Mac user the power to produce graphs that replicate the look and feel of graphs created by professional graphic artists.

 

[fivetoadsloth]

I do quite a bit of computational physics research and understand that getting nice looking plots can be a nightmare.

My program of choice for the research is Mathematica; I'm quite savvy with the language and it is cross platform so I can easily transfer .nb files to my linux box or send them to pc friends. I've used all sorts of plotting programs in the past, however as Wolfram has slowly improved Mathematica's plotting functionality, I find myself doing almost all of my work there. That said, I don't think I've ever produced a figure in Mathematica that went straight into a paper or a poster, I always export to Illustrator and touch up. I realize it isn't the simplest of solutions, but I've found it to be visually appealing and relatively simple. Mathematica is fairly cheap for educational use, often free depending on your institution. Illustrator is a bit more pricey, but there are some free alternatives.

If you'd like some plot examples or notebook files, PM me and I can send you a pdf or a .nb.

 

[radek42]

Origin is an application for Windows users who have much more money than brains. It is much more expensive than any of the Mac options that you named. However, you will be hard pressed to produce a nicer or more professional graph or to perform more in-depth analysis using Origin than using any of the less expensive options.

gnuplot is a CLI application that is used as the graphing engine of other applications. In that role it is fantastic. However, it is not 1993 anymore. You do not need to sacrifice ease-of-use for textbook-quality graphs. If you were a Mac user in 1993, you didn't need it then.

Now for your three options:

1. KaleidaGraph—Hews to the interface paradigm pioneered by the venerable graphing application Cricket Graph. In my not so humble opinion, Cricket Graph's UI was the best UI for a graphing program. In addition to its intuitive UI, KG sports 95% of the power of the most powerful application listed here. This is my primary graphing application.
2. DeltaGraph—During its early days, this application was targeted toward Excel users who needed to produce quality graphs for publication and presentation. There is probably no application available on any platform that can produce prettier graphs. Aesthetics aside, DeltaGraph is comparable in power to KaleidaGraph in its ability to analyze data and to produce science and engineering graphs.
3. IgorPro—I have used this application for decades and have recommended it to others. It is an acquired taste. IgorPro relies on keyboard commands and scripts to perform its work. Its GUI generates scripts that can be edited and extended at will. The scripting language is powerful and easy to use. But, the graphs.... The graphs! IgorPro has a print engine that produces technical graphs as fine as any application anywhere. The demonstrations produce graphs that replicate the pages from technical reference books.
4. QtiPlot—A Qt frameworks-based clone of Origin. Meh. Well, it is free.

Additional applications:

pro Fit—From Swiss developer Quantum Soft, this application features a powerful Pascal-like scripting language.

OmniGraphSketcher—From storied NeXTstep/MacOS X developer OmniGroup, this inexpensive application gives every Mac user the power to produce graphs that replicate the look and feel of graphs created by professional graphic artists.

Thanks for some wonderful comments.

I am still bouncing back and forth. With developers CLI tools rather than full XCode available from Apple I will have gnuplot (and perhaps other linux applications) installed via either MP or fink; leaning towards MP atm As you said, it's perfect as a plotting engine for other apps (fortran in my case). I'd also love to add some quick plotting to Finder as discussed here. So far, no good solution in sight. Perhaps other file browser could do that (muCommander, pathfinder, ?, ? ?

That being said, I figured I could use gnuplot for my plotting needs as well. But no matter how much I like latex I agree ease-of-use of gnuplot is nothing to write home about.

I have to say I tried so many graphing apps recently they all blend together I do not remember KG to stand out for its superior interface, but I'd have look back. I felt reasonably comfortable with IP despite of its many options. I also liked its floating window interface.

OmniGraphSketcher seems like an interesting choice. Although if I have to pay I rather have something more sophisticated For those quick plots the build-in graphing program will do .... except the flaw I mentioned couple posts up.

Thank you again for valuable comments.

R>

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I do quite a bit of computational physics research and understand that getting nice looking plots can be a nightmare.

My program of choice for the research is Mathematica; I'm quite savvy with the language and it is cross platform so I can easily transfer .nb files to my linux box or send them to pc friends. I've used all sorts of plotting programs in the past, however as Wolfram has slowly improved Mathematica's plotting functionality, I find myself doing almost all of my work there. That said, I don't think I've ever produced a figure in Mathematica that went straight into a paper or a poster, I always export to Illustrator and touch up. I realize it isn't the simplest of solutions, but I've found it to be visually appealing and relatively simple. Mathematica is fairly cheap for educational use, often free depending on your institution. Illustrator is a bit more pricey, but there are some free alternatives.

If you'd like some plot examples or notebook files, PM me and I can send you a pdf or a .nb.

Thanks for comments.

I am in physics as well. Mathematica would not be the first thing that comes to mind for plotting purposes. As right now I do not have imminent use for its primary functionality it would pretty expensive graphing application where I am

I also found importing my plots to vector graphics app to finalize it for publication especially composite figures with with insets etc. My choice was Inkscape; all three platforms, good functionality, and its free.

Cheers, R>