Boxplot

Hi,

i was wondering whether there is a help for the BoxPlot feature (could not find it in the manual)…

is there another option for “group x axis” than “whole column”?

for instance i would like to group the x-axis by certain Metadata in order to compare the effect of different treatments on for instance the number of cells per image…
is something like this possible?

cheers, Tischi

Great question. Unfortunately the manual is a little behind when it comes to this feature so I’ll have to enlighten you here.

Basically, the group-by drop down lists “groups” that are defined in your properties file. A group defines a combination of columns that can be used to aggregate the data. There are some examples of groups in the Properties_README.txt.

Basically, the format is:

For example, to create a well group, you might add the following to your properties file:

or a treatment group:

As for grouping by cell count, this is a bit tricky. If you defined a group like this:

You’d end up getting a box plot for every unique number of cells, so if you have images with cell counts between 0 and 400, then you could potentially be creating 400 boxplots. Let me think about this a bit. I suspect there’s a way to finagle a fancy subquery into the SELECT clause, but I’m not sure how. Integer dividing the cell_count by 10 or 20 might work…

So you know, defining groups in the properties file is something that’s on the chopping block. I just need the time to create new controls in CPA that would allow you to specify a set of columns to group by for any given tool, and then you won’t have to predefine these things.

Anyway, hopefully that gets you rolling. Let me know if anything wasn’t clear.
-Adam

OK, unfortunately groups aren’t going to work for you because the query builder is going to try to strip the column names out and it’s not possible if one of the things you’re selecting is CAST(column /10 as INTEGER) but I’ve found a workaround.

open CPA and execute the following query using the query builder tool under the advanced menu (make sure you change the columns and tables to match your own):

SELECT ImageNumber, obcount as count, CAST(obcount/10 as INTEGER) as count_tenth, CAST(obcount/20 as INTEGER) as count_twentieth FROM per_image

save this table to the database File>save table to database …name it “object_counts”

then close CPA, and open your props file and add the following groups:

group_SQL_count_tenth = SELECT per_image.ImageNumber, object_counts.count_tenth FROM per_image, object_counts WHERE per_image.ImageNumber=object_counts.ImageNumber
group_SQL_count_twentieth = SELECT per_image.ImageNumber, object_counts.count_twentieth FROM per_image, object_counts WHERE per_image.ImageNumber=object_counts.ImageNumber

re-run CPA, and open box plot.
Choose OTHER TABLE from the table drop down
Choose object_counts, per_image, NO, OK
Now you can pick whatever measurement from any of your tables and select count_tenth or count_twentieth from the group-by dropdown. The values on the x axis will be 1/10th or 1/20th of the original value.

hi adam,

in fact, the syntax

group_SQL_well = SELECT ImageNumber, Metadata_treatment FROM per_image

covers everything that i need!

awesome!

you guys are really doing a great job with the CP and the CPA!!!

cheers, tischi

Super! I’m so happy the software is working out well for you!

:mrgreen: Adam