Visualization, charts, radar plots and ease of use

Hi,

here my fresh impression on  the Instant-Jchem visualiztion features.

Looking through the forum the topic was brought up in 2008 I guess.

Here some of my random comments based on the PubChem demo project

1) From an EXCEL or statistical software point of view (Statistica or WEKA)

I would suspect you activate a column and it would draw a histogram

or you would activate multiple columns and it would ask: what is x, what is y?

That could be done with a right click.

I could not find any of them, not in View menu, Tools menu, visualize menu. I installed all the standard plugins, nothing there. I activated single columns did a right click (ala draw) nothing. So my conclusion, introducing the term widget (what is a widget anyway) instead of just allowing to plot graphs is counter-productive. Its not how the average chemist (me?) would work.

---

Not sure what went wrong, maybe PubChem demo db does not have graphs, maybe I should use JChem for EXCEL, maybe databases natively do not allow graph.

Finally I came to activate the DESIGN mode and was able to include a histogram and X,Y diagram

but only for the query mode or the single molecule view mode.

So basically what I expected was to be in Grid View and  with a single right click to draw x,y graphs of properties and view histograms for a series of compounds. Basically a little button that exactly does the same as in design mode but for many molecules and in an easy way. I would be interested how other users see that.

Cheers

The best starting point for understanding the charts is the 'Wombat (charts overview)' form which is present in the 'Wombat (compounds view)' data tree in the standard demo data project that is included in IJC.

There is also a nice overview from Chris Swain that can be found here:
http://homepage.mac.com/swain/Macinchem/Reviews/ijc_review/ijc_plots.html

The most important thing is that they work with forms. You design the form to include the widget types you want, and configure each widget in terms of its data fields and display properties. Details can be found here:
http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/managing_data/widgets/VizWidgets.html

Tim

Hi Tobias,

beside what Tim have described, if I understand you correctly you would like to have more possibilities how to create a chart and how it should behaves:

1. chart with statically bound field(s) - that's how it is implemented in current(5.5) IJC version


2. The scenario you've describe - ability to create a dynamically bounded chart which would change bound fields according to a table columns selection with which it would have to be linked somehow.
   
   It would be possible to create such chart via popup-menu of a table (possibly other multirow widgets).
   
   That's sound interesting. Might be such charts in general could be bound to field(s) just by dragging table column and dropping them into a chart. E.g. you would drag and drop "Mol Weight" column and drop it into the existing histogram which would react accordingly.
   
   Surely there is a need for some smooth, unambiguous UI. I'll file a new RFE for it.

Thanks for the feedback.

Hi,

I agree with Tobias, the way plotting has been implemented is too static. Being able to create a plot on the fly from a query result would be the way forward. Drag-and-drop facilities for choosing what to plot would also be an enhancement.

The both scenarios are filed in our issue tracker. Very likely they will not be part of 5.6 (next) release (due to other already planned features). We will try to come with something in the future release and come back with result here. Thanks for the ideas.

mkrauskopf wrote:

chart with statically bound field(s) - that's how it is implemented in current(5.5) IJC version The scenario you've describe - ability to create a dynamically bounded chart which would change bound fields according to a table columns selection with which it would have to be linked somehow. It would be possible to create such chart via popup-menu of a table (possibly other multirow widgets). That's sound interesting. Might be such charts in general could be bound to field(s) just by dragging table column and dropping them into a chart. E.g. you would drag and drop "Mol Weight" column and drop it into the existing histogram which would react accordingly.

Martin,

thanks for your ideas, there is nothing wrong with a static design. But in terms of "ease of use" a more direct way would be "easier". Also consider the background of program use, you can bet that 99.9% of the chemists know how to use EXCEL, so making it similar would be one way to make it easier.

Be it a little graph button on the top, or a grap menu under tools, or a graph option with a right click. Here the user should be able to pick x,y-graph, histogram or any plot you provide.

The option you suggest is even easier, by dragging one or more header columns into a graph area and then a plot and option would occour.The question is, will users figure that out, is there an intuitive option in a menue, or an intuitive button somewhere, if not you have to tell them. 

Other than that I think compound selection via graphs is a very powerful feature, especially with an activation button, so you can drag the cursor around  compounds and they are activated or can be excluded.

Thank you!

Tobias

Hi Tobias.  In future releases we are going to talk about priorities and ways how to enrich IJC visualization. So feedback and point of view from real users is always welcomed. We will go through your points and come back with results/ideas/questions... Thanks.

Hi,

Any chance of sliders for property ranges in plots like in SpotFire?

Cheers!

HomerE wrote:

Any chance of sliders for property ranges in plots like in SpotFire?

Hi Homer. I'm not sure what exactly do you mean by "property slider". I do not have SpotFire.

Do you mean that properties accessbile in a chart customizer would be accessbile directly in the top-level window (like e.g. "Projecs" window is) and you could directly manipulate all the properties with real-time reflection in chart widget? If yes, we are thinking about something like this for quite some time for all IJC widgets in general. Not sure whether we get to it in the next release (not possible in 5.6 (next release) time-frame).

In the mean-time notice that you might perform at least zooming and panning with mouse.

Hi,

Spotfire (the gold standard of visualization) see online demos here: http://spotfire.tibco.com/demo/

allows the use of sliders and toggle buttons and all kinds of interactive options to refine graphs.

I guess for Instant-JChem use, A) the filtering via the graphs itself is an option  and of course B) the query filter of mulecular properties itself.

Having sliders or two-range sliders (min-max but movable) are certainly very easy to use. Not sure how interactive that would be for a large DB, but for smaller projects that would be the deluxe version and really nice.

 

Cheers

Tobias

I saw Spotfire in action on European UGM... did not realize there are the demos available online. Thanks.

Spotfire's Filters window is very usable, no doubt. In IJC It would not apply to charts only but to all widgets. I've filed another RFE in our tracker. Again, we will  get back here when we have something. So many ideas, so little time... :)

Spotfire-style sliders are attractive, and are certainly on the wish list. Though it should be pointed out that the way IJC and Spotfire work are slightly different, which impacts this quite significantly.

Spotfire sucks all the entire data into an in-memory data model, and so can provide very fast and efficient filtering. In contrast primary use of IJC is for reporting from a central (e.g. Oracle) database that is on your network, with a potentially slow network connection, and IJC uses an "only when  needed" approach to grabbing the data from the database (this way, when viewing data in grid view for 1 million rows, only the visible rows are necessarily retrieved from the database). This makes dynamic filtering  impractical as the data is not directly accessible and will require round trips to the (slow) database, which would just not work well for a dynamic filtering appoach.

That said, the approach is attactive, and you could imagine slider widgets on a form that you could use to control selection of data. But to do so you require all data required for filtering to be sucked down from the database into memory, which itslef leads to lots of complications, which is why this type of functionality is not yet supported.

Tim

Thanks Tim,

that makes sense speed wise, many of the proposals sound very easy, at least the ideas,

slider here, button there, but once you look under the hood of the machine, it looks quite different :-)

Tobias