Aabel 2.0 - Scientific Plotting and Data Analysis

Scientists of all sorts require advanced graphing/plotting to explore and present data. Not everything can be jammed into a program like Excel or standard spreadsheet or business graphing programs. Our Windows-using colleagues often use programs like Origin or SigmaPlot. On the Mac, plotting programs include Kaliedagraph, Igor Pro, DeltaGraph, pro Fit, ChartSmith, and Aabel.

Aabel is a powerful program along the lines of Origin and SigmaPlot, offering plotting, statistical analysis and curve fitting. To quote the documentation, it's designed for "statistical analysis with a focus on visualization, dynamic data exploration, powerful data management, and interactive scientific graphing."

After several years of development since version 1.5.x, Gigawiz has released a major update of their program Aabel. Updates include a universal binary for Intel Macs, full Unicode support, a new statistics analyzer mode, AppleScript support, new plot types, as well as more minor improvements such as import of data from dBase, Matlab, and Splus. For a full list, check out Gigawiz's What's New documentation.

There's also now a Quick Start guide, which offers quick tutorials on running the new statistics analyzer, creating a standard X/Y scatter plot, curve fitting, and customizing charts.

This review cannot possibly cover every feature in a package like Aabel. Instead, it is offered to cover some major features, some drawbacks, and to describe Aabel's unique approach to scientific data visualization and exploration.

Plotting

Aabel offers many unique statistical and data exploration features. One key of the program is the "pipeline" approach to data. (This includes plotting, statistical analysis, and data filtering.) To create any sort of plot, choose "New Visualization & Statistics Pipeline". If more than one worksheet is open, you can pick one or more worksheets to include in plotting. The new plotting window offers a blank page, with a gallery of button menus for graphs along the top. Picking a particular graph type will also bring up a palette for choosing variables and some plotting options.

Once the graph appears, this approach makes it extremely easy to explore multivariate data by flipping through different variable combinations in the side palette -- the plot will update automatically.

Similarly, for contour, 3D or histogram plots, the palette offers the ability to dynamically change the number of bins. Added in this version is the ability to manually set the size range of the bins instead, although this is still lacking for contour plot levels.

Interactivity with the pipeline model also allows clicking, brushing, selecting in plot to result in selections in the worksheet itself. This also allows customizing the point markers used for these particular points via the various controls to the left of the row. These alter the visibility (for filtering), color, style of marker, and labeling options. The intent appears to allow easy identification of outlier points and general data exploration, and this works well.

Aabel offers a wide range of scientific and technical plot types, from standard bar, pie, and scatter plots, to statisical box and wisker, histogram, contour (from XYZ data or a matrix representation), to a variety of geographic and mapping plots. This version helpfully offers the button menus along the toolbar of a visualization pipeline, but also a gallery button which categorizes plots and offers textual descriptions of each type. Unfortunately, many of the descriptions point the user directly back to the PDF user's guide. Some form of hyperlink or integration between the two sources would be helpful here.

Plot Formatting

Many graphing/plotting programs also bring up a new plot in an individual window. Since Aabel uses a page-layout approach, it is easy to add multiple plots to the same page window. On the other hand, the default plot sizes may look slightly small on-screen. If you wish to enlarge a plot, you should choose the graphics select (pointer) tool, and stretch the frame as you might in a drawing program like Canvas, Illustrator, PowerPoint, or Keynote.

Of course Aabel also offers some drawing and annotation tools, including text boxes, lines, rectangles, circles, and the like. Strangely, in order to create an arrow, one must draw a line to the point, select the line with the graphical selection tool, and then set the arrow options in the toolbar.

Overall, Aabel offers a huge variety of plot customization options and very professional quality scientific graphics. Graphics exports are to PDF format, allowing smooth resizing in many Mac programs like Keynote or Pages. Unfortunately, copying or exporting as a PDF graphic makes it impossible currently to paste into Microsoft Word or PowerPoint directly. Support for exporting as PICT, PNG, TIFF, or other graphics format would be helpful in sending the graphics to colleagues or using Aabel with Microsoft products.

Statistical Analysis

Not to be left out in any scientific plotting program are features for error bars, curve fitting, and statistical analysis

Once a chart has been plotted via a visualization pipeline, curve fitting can be performed. Aabel gives the option for a normal regression, or a customized regression for a partiuclar variable pair (e.g., for a custom user-defined function). The former allows linear, polynomial, and other typical regression techniques, while the latter offers a libary of various functional forms and the ability to write out a custom functional fit. Aabel also offers the option to include confidence bars for linear regressions. (This would be a welcome feature in many other programs to give error bars on the regression itself.)

Additionally, Aabel offers a full range of statistical analysis from a visualization window by the "Statistical Analyzer" mode. This includes regression techniques included through curve fitting, albeit with the option of creating a new worksheet with predicted regression values and residual errors. Also included are a wide range of standard statisical methods and you will be guided through the analysis in the analyzer window, with the option of displaying results in the window or output into the plot window itself.

Interface Quirks

Unfortunately, Aabel often doesn't present things in a completely user-friendly manner. This means that there's definitely a learning curve when initially using the program.

For example, unlike most spreadsheet applications, setting a formula for a column of data requires you to not only enter the formula in a pop-up dialog, but click the "Calculate" button. The data is not updated until you open the dialog and re-click "calculate." Unlike the dynamic pipeline structure in the rest of the program, calculated data in a worksheet will not be updated dynamically.

As another example, to set the numerical format for a column of data, there is no menu command to do this. Instead, you should click the unlabeled rectangular button above a column. (A tooltip does pop up after about 4-5 seconds explaining that this is the "variable properties" button.) Here you will see some useful bits, including a histogram of the variable and various statistical properties. In addition you can set the numeric format (e.g., scientific), the number of decimal places, etc.

Changing the properties of a graph can also be frustrating in comparison to many other Mac plotting packages. Aabel offers a variety of selection tools. Some select data points (e.g., for filtering or labeling). The regular arrow tool is a graphical selection tool used for selecting and moving parts of a graph around on the page. To change the axis options, you must use the rectangle or lasso data selection tool, then mouse to an axis edge and double-click or bring up the contextual menu. Once there, version 2.0 brings up an improved dialog with buttons/tabs dividing the formatting options into separate pieces. (Previous versions showcased all axis formatting options in one huge, complicated window, so this is a major improvement, even if it's still a non-traditional approach to a tabbed dialog.) Also, version 2.0 allows formatting the axis via a menu option, which is a welcome addition.

Another annoyance comes when trying to copy graphics from the program into another program. Currently, this copies everything visible in the visualization pipeline window. Clicking on one or more objects and copying yields the same result.

My point is not that Aabel is necessarily hard to use, just that you may find yourself needing to search through the PDF manual to find out what you need to do. If the developers made some common functionality available through multiple paths (e.g., menu items, contextual menu, etc.), this would probably help. As described above, the chart axis formatting menu option is a welcome example of this. I also wonder if the data selection and graphical selection tools could be combined in some fashion.

Summary

Aabel offers a huge variety of scientific plotting, data exploration, and statistical analysis tools. Its interface requires some learning curve. The developers would do well to provide multiple ways to access key dialogs (e.g., graph and numeric formatting settings) and spend some time getting feedback from new users to make the program more intuitive. The degree of interactivity gained via Aabel's pipeline model makes analyzing correlations in multivariate data a breeze. On the whole, it offers excellent graphic quality for plots, and a range of indespensible statistical and data exploration tools for scientists.

Aabel 2.0 sells for $445 per license, $345 for Educational users, with discounts for larger quantities. Upgrades from previous versions are $195 per license. A free 30-day demo is available with no limitations.

Example Plots

Contour Plot

Histogram Plot

Regression Plot

Comments

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Export formats

I'm not sure why one can not use pdf with Word? I use pdf with word all the time, just drag the single page pdf straight onto the Word document.

What I have not yet been able to do is make an Aabel chart with a transparent background so when I use the PDF in say Keynote I can keep a simple gradient background.

BTW opening up the PDF file in Preview allows you to save it in all of the formats you asked for.

PDF and word

I have had problems with this in the past, if I remember correctly, if you cut and paste the PDF gets converted to a bit mapped image which can result in a loss in quality. Another issue I've come across is that some fonts do not transfer well.

Word and cut and paste

From my experience, you do not want to cut and paste graphics into any Microsoft product. This is especially true if you are going to be exchanging the file with people in the Windows world. Best to get in the habit of using the "insert graphic from file" function.

Comments from Aabel Developer Team

The developers of Aabel have kindly offered some comments on the review, and have signed up to MacResearch so they can field any additional comments or suggestions that are posted to this thread.

Here are their comments in full.

First of all, we find the review helpful and constructive, appreciate the comments, and would like to thank the reviewer(s). For general discussions on Aabel, or ways that we can improve the application ease of use, we’ll be happy to participate in the discussion in the thread. However, please note that there are a few statements in the review, which are not correct (easy to overlook when reviewing a large application like Aabel in a short time), and it would be much appreciated if some editorial corrections could be made.
(a)
Under the topic of “Plotting”, it is stated:
“Unfortunately, copying or exporting as a PDF graphic makes it impossible currently to paste into Microsoft Word or PowerPoint directly. Support for exporting as PICT, PNG, TIFF, or other graphics format would be helpful in sending the graphics to colleagues or using Aabel with Microsoft products. Support for exporting as PICT, PNG, TIFF, or other graphics format would be helpful in sending the graphics to colleagues or using Aabel with Microsoft products.”

-PDF is the default export and copy format in Aabel, not the only format. While in the Quartz mode, Aabel can export PDF, or bit images (TIFF, PNG, JPEG, PICT, SGI, Photoshop, PICT). However, a PICT and other bit images generated via Quartz do not support an alpha channel and will be opaque. Hence, Aabel also provides a graphic switch to permit switching between the Quartz and QuickDraw graphic systems. While in QuickDraw mode, exporting as PICT or copying generates a vector drawing.

(b)
Under the topic of "Plotting", it is stated:
“Added in this version is the ability to manually set the size range of the bins instead, although this is still lacking for contour plot levels.”

-That was a limitation in the previous version. In the current version, manual binning of contours is available for both matrix and X-Y-Z contour charts.

(c)
Under the “Interface Quirks”, it is stated:
“As another example, to set the numerical format for a column of data, there is no menu command to do this. Instead, you should click the unlabeled rectangular button above a column.”

-There is a menu command for modifying the numeric or date/time format. The command is: Worksheet > Set Variable Data Format > For Numeric Variables / For Date & Time.

(d)
Under the “Interface Quirks”, it is stated:
“Another annoyance comes when trying to copy graphics from the program into another program. Currently, this copies everything visible in the visualization pipeline window.”

-This is not the case. Copying and exporting can be done for all viewer contents, or for contents of an enclosure. The latter is done by enclosing the item(s) in a rectangle, selecting the rectangle and using the contextual menu (documented in the manual). However, we see that this can be confusing. Hence, we will in the next update allow copying or exporting of selected objects (directly) and add drag and drop for copy and paste into applications that support the action.

(e)
Under the “Interface Quirks”:
In the context of “Changing the properties of a graph can also be frustrating in comparison to many other Mac plotting packages….”, it is stated:
“To change the axis options, you must use the rectangle or lasso data selection tool, then mouse to an axis edge and double-click or bring up the contextual menu.”

-This was a limitation in Aabel 1.5.x, but in Aabel 2.0 there are four ways of accessing the axis dialog (which is documented in the manual). The other three ways that were added to Aabel 2.0, are:
(i) From the main menu (Viewer > Chart Axis > Open Axis Dialog)
(ii) Pressing Cmd+Option+F7
(iii) Clicking on any axis dialog and using the contextual menu

(f)
Under the “Interface Quirks”:
One feature of Aabel that has been discussed as an interface quirk is the separation between the data selection and graphical selection modes.
In applications that allow selecting/deselecting a chart pane or other graphic objects, but do not allow selecting plotted data to operate on attributes that are hot-linked to data sources (e.g., traditional graphing apps), or in applications that allow selecting data points and data brushing, but do not have a need for selecting static objects (e.g., pure exploratory data analysis apps), the program can use a single selection mode. In applications (like Aabel) that allow selecting plotted data/data regions to operate on attributes that are hot-linked to data sources (e.g., performing data brushing, changing source markers, generating subsets of data, excluding and including data on the fly, etc.), and also allow selecting objects to operate on static aspects of graphics (such as moving, resizing, aligning, etc.), using a single selection tool will result in interference between the two completely different operation types. This is why the data selection and graphical selection tools cannot be combined. Having two selection modes in Aabel is a necessity for combining a full-featured graphing application with a full-featured exploratory data analysis application.

(g) Under the “Summary”:
- It is emphasized that we should provide multiple ways to access key dialogs (e.g., graph and numeric formatting settings). Please see points (c) and (e) above. Aabel had quite a bit of limitations in the previous version, but in 2.0 for accessing any main dialog, there are multiple ways. However, due to diversity of functions, perhaps we should provide a few pages/tables of what different commands do.

We are totally open to suggestions and in fact, many new features and improvements in Aabel 2.0 are based on users feedback. Regarding the point of making Aabel more intuitive, we are seeking continuous improvements. One thing we cannot do, is to make Aabel behave similar to pure graphing applications, which as explained in the point (f) above, is in conflict with combining a full-featured graphing program and a full-featured exploratory data analysis program in one app.

Additional Comments

I'm glad to see some comments from the developers. It's nice to have a review in a format like MacResearch where we can have a more extended discussion.

(a) Exporting Graphics.

OK, upon further study, you can export in these other formats, but it's a little non-intuitive. By default, the graphics export command in the File menu is PDF. No other option is available in the export dialog. However, if you try the "Preferences" command, you can set the export to a Bitmap format -- and then these formats are available in the dialog.

Again, this is a little non-intuitive. It would be nice if PDF and bitmap options were both available by default without needing to resort to the Preferences dialog. OmniGraffle or Preview are good examples of this.

(b) I used the trial version of 2.0.3 for the review. I see no option to set the contour width rather than the number of contours for an XYZ plot. Since I prefer to have specific contour levels, this would be appreciated.

(c) This menu item has been disabled for every column of every worksheet which I've tried. How should I use it? Otherwise, this would be greatly appreciated.

(d) For example, if I copy a graph, even if the legend is not selected, it automatically comes along. If the legend and graph are independent objects, it seems strange to me that I cannot copy the graph but not the legend -- unless I hide the legend. Perhaps this is an unusual request, but to me, copying the legend when it was not selected seemed strange. Granted, the default is probably correct -- a graph isn't very useful without a legend.

(e) Great. I had not seen these options, but this is definitely along the lines I suggested. However, the graphical selection tool has no contextual menu item for the axis dialog.

(f) I understand the philosophy behind Aabel's design and use of two types of selection tools. However, I do believe that this creates a learning curve for most users.

For example, I can imagine that the data selection tools could function identically to the graphical tool when the user clicks on a line, arrow, text box, etc. Similarly, if the user clicks on the axes or tick marks or labels (i.e., no data is selected), why can't the data selection tool change based on the context and function identically to the graphical tool?

As I said, I do understand the design philosophy. Once you understand the distinction between the two tools and the functions assigned for each, they work well. However, I personally believe some careful thought and programming could eliminate the need for a separate graphical selection tool.

(g) A few pages/tables describing different commands would be most welcome in the user's guide or quick start. I also believe that the menus are a bit large -- for example, rather than having separate items for "Bring to Front" and "Bring Forward," couldn't the menu item change name when the user holds down the shift key?

This sort of dynamic menu is used in many Mac programs and would help simplify and organize the menus. I admit I certainly did not find some of the menu items you described, and in some cases they appear disabled (e.g., point (c)) for reasons I don't understand. Added information in the manual and help system would be greatly appreciated.

Again, I'm glad to see such a responsive developer team. I think Aabel is a great program for Mac researchers and hope to see continued improvement. Version 2.0 is definitely a worthwhile upgrade over 1.5.x.

Transparent Backgrounds

At least in version 2.0 (as reviewed), this isn't hard. Most graphs have transparent fills anyway (just copy from Aabel and paste into Keynote).

But also...
* Click on the "Graphical Sublayers" palette (in the toolbar or from the Window menu).
* Click on the "Transparency" tab. Pick the graph you want and edit the transparency levels for axes, fill, markers, etc.)

Export/Copy Compatibility With Word and PowerPoint

There is a difference between allowing import of PDF and the nature of embedded graphics that are inserted/imported into an application. In applications that fully support native PDF (e.g., Keynote, Preview, Acrobat, Aabel), imported PDF is embedded as PDF collage (vector graphics). Word and PowerPoint render a PDF into a bit image. A bit image has a lower quality than a similar vector graphic, is poorly scalable, can produce jagged edges, and is commonly rendered opaque (e.g., PowerPoint transforms any color other than white as opaque). Therefore, a PDF image that looks great when imported into applications such as Illustrator, Keynote, Preview, Acrobat, can (in comparison) look poor quality when imported into Word or PowerPoint. However, importing a PICT collage (not a bit image PICT) into Word or PowerPoint produces very good quality vector graphics.

The main problem with using PICT collage on a Mac is that fewer and fewer QuickDraw fonts are available in the System, which can create font metrics and encoding problems during export. It is also important to notice that PICT collage is generated with QuickDraw commands, and cannot be produced if an application offers only Quartz (Core Graphics). Aabel provides a graphic switch that can be used to export or copy graphics in either Quartz or QuickDraw mode. If you want to export or copy graphics for use in Office products, switch Aabel to the QuickDraw mode (under Aabel Preferences, Click “Quartz/ QuickDraw Options", and uncheck the “Use Quartz for 2-D Graphics”. To switch back to Quartz, uncheck the checkbox. The graphic switch in Aabel is provided to allow export and copy of vector graphics for use in Word and PowerPoint.

Another issue is the choice of resolution for export and copy. High-resolution graphics produce good quality print output, but can be unsuitable for on-screen viewing, because the result depends on the downscaling algorithm used by the rendering engine. The topic of copy and export and how to achieve the best results for different purposes cannot be covered in a short discussion, and warrant an article by itself.

New version of Aabel

Aabel 2.1 was just released.

This update Includes:
- Support for drag & drop from Aabel into applications that support the operation (e.g., Keynote, Word, PowerPoint, Photoshop, etc.)
- Support for drag & drop from other applications (e.g., LaTeX Equation Editor, graphic files from Finder, etc.) into Aabel
- Enhancement of UI for use of diverse export formats (PDF, PICT vector graphics, PNG, BMP, JPEG, TIFF, bitmap PICT, SGI, TGA, etc.)
- Added flexibility in 3-D and 4-D scatter charts, to allow graphic clipping without a need to exclude data from the visualization pipeline
- A fix for a bug that had been introduced in the 2.05 build, interfering with conversion of the 1.5.8 viewer files

Preferred software: DataGraph

Aabel has an astronimical price tag.
For most graphs I now use DataGraph (www.visualdatatools.com)
It's a cheap alternative, albeit not so powerful as Aabel

DataGraph

I'd agree. When I wrote this review, DataGraph didn't exist. I'll review it sometime soon.