Manually set min/max on the axis // coloring scatter plots

Hello everyone, I have two of small questions related to displaying data with CPA2:

  • Question: is there a way to manually set min/max on the axis? Let’s say, I have two databases and would like to compare histograms of the same variable using the same range. Currently, every histogram-window ends up having its own min/max axis.

  • Question: is there a way to color a subset of dots in a scatter plot? When I show variables X vs Y on the scatter plot but I would like to color code the dots based on variable Z … or at least based on a filter. In my case I have virus infected cells and cell which are not infected. Maybe one could do something like this for a common scatter plot:
    - for all Z<z0 -> show corresponding dots in green
    - for all z>=z0 -> show corresponding dots in red.

Thank you for your help

P.S: I noticed a small inconsistency: in histograms, displaying a log(variable) results in an axis number annotation of “4 … 7” and the unit anotation is “log(variable)”. Whereas with scatter plots, displaying a log(variable) results in an axis number annotation of “2^5 … 2^9” and the unit annotation is “variable” only. It would be great if both had the same type of annotation for both number and unit.

Hi,

Sorry for late response.

[quote]- Question: is there a way to manually set min/max on the axis?
[/quote]

No unfortunately the visualization is pretty limited. We don’t have funding for extra features for CPA at the moment, and besides the toolbar buttons in the Histogram window, there are no other zoom or scaling functionalities. You could try KNIME, Matlab, or R for other more full-featured post hoc analyses: cellprofiler.org/interfaces.shtml

Hmm, no I don’t believe you can show both of these at the same time on a Scatterplot. As you indicate, you can create filters and remove points, but you cannot plot them at the same time (afaik).

And thanks for the report on the “log()” annotation. We’ll add that to our list and hopefully someday we can add it!
github.com/CellProfiler/CellPro … /issues/63
Cheers,
David