BookmarkSubscribe
Choose Language Hide Translation Bar
FantaBola
Community Trekker

Tracking a 96-well over time

Hello,

 

I have a kinetic assay that records OD over time on a 96 well plate.

The output is OD and I have data columns with time and location (A1, A2 etc) for each OD value.

By applying the map shape I can visualize the 96-well plate in Graph Builder on a certain time (e.g. at 0 or 1 hour).

 

Would it be possible for Graph Builder or another SAS JMP feature to show the development of OD over time on the same plate (similar to the Bubble Plot function) ?

0 Kudos
1 ACCEPTED SOLUTION

Accepted Solutions
ih
ih
Community Trekker

Re: Tracking a 96-well over time

To expand on Ian's answer, you can add a local data filter to your graph, change your time axis to ordinal if you want to see discrete sample times, and then use animation under the data filter. If you run the script below you would just need to press play in the upper left:

 

Names default to here( 1 );

dt = Open( "$SAMPLE_DATA/Time Series/Air.jmp" );

Column( dt, "date" ) << Set Modeling Type( "Ordinal" );

graph = dt << Graph Builder(
	Size( 516, 680 ),
	Show Control Panel( 0 ),
	Variables( Y( :Ozone Concentration ) ),
	Elements( Bar( Y, Legend( 3 ) ) ),
	Local Data Filter(
		Add Filter(
			columns( :date ),
			Where( :date == 1953936000 ),
			Display( :date, Size( 256, 360 ), List Display )
		),
		Animation( Animate Column( :date ), Animate Rate( 90 ) )
	),
	SendToReport(
		Dispatch(
			{},
			"Ozone Concentration",
			ScaleBox,
			{Format( "Best", 9 ), Min( 0 ), Max( 10 ), Inc( 2 ), Minor Ticks( 1 )}
		)
	)
);

play.PNG

 

13 REPLIES 13
ian_jmp
Staff

Re: Tracking a 96-well over time

Get your Graph Builder display the way you want it, then try adding your 'time' variable to the local data filter.

ih
ih
Community Trekker

Re: Tracking a 96-well over time

To expand on Ian's answer, you can add a local data filter to your graph, change your time axis to ordinal if you want to see discrete sample times, and then use animation under the data filter. If you run the script below you would just need to press play in the upper left:

 

Names default to here( 1 );

dt = Open( "$SAMPLE_DATA/Time Series/Air.jmp" );

Column( dt, "date" ) << Set Modeling Type( "Ordinal" );

graph = dt << Graph Builder(
	Size( 516, 680 ),
	Show Control Panel( 0 ),
	Variables( Y( :Ozone Concentration ) ),
	Elements( Bar( Y, Legend( 3 ) ) ),
	Local Data Filter(
		Add Filter(
			columns( :date ),
			Where( :date == 1953936000 ),
			Display( :date, Size( 256, 360 ), List Display )
		),
		Animation( Animate Column( :date ), Animate Rate( 90 ) )
	),
	SendToReport(
		Dispatch(
			{},
			"Ozone Concentration",
			ScaleBox,
			{Format( "Best", 9 ), Min( 0 ), Max( 10 ), Inc( 2 ), Minor Ticks( 1 )}
		)
	)
);

play.PNG

 

FantaBola
Community Trekker

Re: Tracking a 96-well over time

Thank you for your reply.

 

It was easy to re-write the script to my case and add my wells under Shape.

I have added the output below 

 

 96 well.PNG

ih
ih
Community Trekker

Re: Tracking a 96-well over time

I am glad that worked. How did you draw the circles in your shapes? They look nice!
0 Kudos
FantaBola
Community Trekker

Re: Tracking a 96-well over time

I did not draw them. JMP have developed JMP-files with the 96-well and 384-well format. You can then add them under Map role in column properties.

0 Kudos
ih
ih
Community Trekker

Re: Tracking a 96-well over time

So they do, thanks!

0 Kudos

Re: Tracking a 96-well over time

The shape files for the microtiter plate wells can be found in here in the JMP File Exchange area of the JMP Community.

Learn it once, use it forever!
0 Kudos
ranjith94
New Contributor

Re: Tracking a 96-well over time

Hi Mark,

I tried to make change 96 well plate design according to my plate design, which is 10*10 and 4 wells left empty in the middle. But my out put is showing empty graph. Is it possible to use this graph for producing heatmaps for multiple variables.

 

Capture.PNG 

0 Kudos
Highlighted

Re: Tracking a 96-well over time

So, you made your own shape files for your 10x10 plate layout? Did you follow the steps described in this blog post?

 

So, you can add the new shapes to Graph Builder but your response data (Y) does not appear? Did you drag the data column with the response data into the middle of Graph Builder? Did you follow the steps described in the blog post mentioned above?

Learn it once, use it forever!
0 Kudos