Charting assay results grouping by DerivativeType

LabKey Support Forum (Inactive)
Charting assay results grouping by DerivativeType Anthony Corbett  2013-05-06 13:32
Status: Closed
 

I have some assay results which have the same Participant/SequenceNum but have different Primary/Derivative Types. After I copy these results to the study I can add in the Primary and Derivative Type Columns from the Specimen Repository into the DataGrid. However, when I go to chart these results as a time series the Primary and Derivative columns are not available under the measures options for "Divide data into Series: One Per Participant and XXXXXX".

Am I not copying the results correctly to the study or do I need to configure something else to be able to use Primary/Derivative columns as dimensions?

Thanks,

Anthony
 
 
cnathe responded:  2013-05-07 07:06
Anthony,
It looks like we currently only consider the columns/fields from the base query/dataset when providing a list of available dimension options for the time chart.

However, I believe that you can create your desired chart using the following steps:
1. create a custom query over your base copied-to-study assay dataset in the study (see attached query example using a NAb assay)
2. write the query so that it includes the Primary/Derivative fields you want to use plus the measures you want to plot from the assay dataset
3. create a Time Chart over that custom query
4. if the Primary/Derivative columns don't show up as available dimensions, go back to your query and edit the metadata to set those fields as data dimensions

Give that a try and let me know if it does not work for your scenario.
Thanks,
-Cory
 
Anthony Corbett responded:  2013-05-08 13:40
Cory,

I created the custom query of the copied-to-study assay dataset and added in a computed column "ResultType" which is the dimension I want to use to put my the data series into groups (this is actually a concatenation of 2 dimensions as the charting wizard only allows creating data series by a single dimension). See attached picture of SQL source.

However, when I go to create the time chart it errors that there is no measures to choose from in my custom query; see attached picture of error. This is not the case as there are fields in the metadata marked as meaures; again see attached picture of metadata.

When I look at the response from VisualizationController.GetMeasureAction none of the measures from by custom query show up in the JSON response...

Please let me know what I'm doing wrong.


-
Anthony
 
Anthony Corbett responded:  2013-05-08 13:49
I just looked at the help for the choose measure and it said it needs ParticipantVisit and then I looked at your example SQL with the same comment.

I'm all set... thanks!

-
Anthony
 
cnathe responded:  2013-05-08 13:50
Anthony,
Try including the gc.ParticipantVisit field in your custom query SQL. For custom queries to work with the time chart, both the ParticipantId and ParticipantVisit columns are required so that the time chart code knows how to join data between datasets/queries.

We tried to add a little bit of help text to this extent (see attached screenshot), but couldn't think of a great place to put this information.

-Cory
 
Anthony Corbett responded:  2013-05-08 14:10

Will this time chart based on a custom query auto update when new data is copied to study from the assay?

I tried copying more data but the chart didn't update, I had to re-create it.
 
cnathe responded:  2013-05-09 06:39
Anthony,
The time chart is re-rendered each time you open the report based on whatever new data is in the base query/datasets. However, the set of participants or groups selected for the report is saved with the report metadata. So, when you copied new assay data to the study was for new participants or was it new data for existing participants?
-Cory
 
Anthony Corbett responded:  2013-05-15 08:29
Sorry I didn't back to you right away.

Yes, I copied new data that added a new filter. So I had to go edit the chart and check the new filter and save it again.

Thanks again for your help.

-
Anthony