Comments on: Burtin Antibiotic Illustrations

By: xan

xan — Thu, 29 Jan 2009 23:24:11 +0000

Nikhil, Thanks for sharing your class assignments. Some are quite creative. It would be interesting to see a similar exercise done at the end of the semester.

By: xan

xan — Thu, 29 Jan 2009 23:22:55 +0000

Thanks for the feedback, Dave. Good idea on making the staining be an X variable to get two columns of markers. It’s usually best to avoid duplication (by indicating the staining by both color and position), but I tried your idea and I think it the duplication adds emphasis to the message.

I made the entry in Graph Builder, which was new in JMP 8. First I had to “stack” the three antibiotics columns into a single column with three levels. Then I used that as a grouping variable. The basic script was

Graph Builder(
Show Control Panel( 0 ),
Variables( Y( :MIC ), Group X( :Antibiotic ) ),
Elements( Points( Y, Legend( 2 ), Jitter( 1 ) ) ));

But that doesn’t include the log scale customization or the dose line customizations.

By: DaveG

DaveG — Thu, 29 Jan 2009 07:37:25 +0000

I had a go at this at home with JMP and it did a nice cell plot (heat map) split by gram status and antibiotic.
But I wanted to says liked I like your submitted plot best. On the plots I did I reversed the scale so the measure is related to ‘antibiotic effectiveness’ but I think you are right – the crucial questions are:
which antibiotic to choose?
what dose to give?

For this I would add something like a 90% or 95% quantile as the line in your diagram so x% of bacteria have a MIC below that, then the Dr can chose accordingly, given knowledge or ignorance of the gram status of the infection.

In your diagram it is unclear what the horizontal lines are,
I think I would try putting the gram neg & positive status bacteria in separate columns within the boxes.

If you used JMP for these plots would you consider publishing the code?
I am just learning it and looking for good worked exercises .-)

Dave

By: nikhil

nikhil — Sun, 18 Jan 2009 22:03:02 +0000

pretty cool visualizations!

Data Visualization course at Stanford also worked on the same visualization as an assignment, you can find the submissions here – https://graphics.stanford.edu/wikis/cs448b-09-winter/Assignment1