Question: on extend_val parameter in parseWorkspace
0
3.5 years ago by
lovetatting10
Sweden
lovetatting10 wrote:

Thanks for a great package!

I've had some problems I've managed to fix by tweaking the extend_val parameter of parseWorkspace.

I would sometimes get an error "try to extend the coordinates for ellipse gate!". I think this emerged from line 320 in gate.cpp. I didn't understand it at first, but it was urging me to adjust the extend_val parameter as the actual coordinates of the gate that caused the error, were smaller than the extend_val.

I also had different values in gate counts from flowCore and FlowJo, and the gates in plots (from plotGate) would suddenly snap out as a straight line to the edge.

I fixed it by setting extend_val to -Inf and haven't had these problems since. I can't find a performance penalty or other side effects, but I guess there is a small performance penalty. Maybe this problem was specific for me. Just thought I'd share as this has been bugging me for some time. If there is a recommended way, I'd be happy to learn!

flowworkspace • 548 views
modified 3.5 years ago by Jiang, Mike1.2k • written 3.5 years ago by lovetatting10
Answer: on extend_val parameter in parseWorkspace
0
3.5 years ago by
Jiang, Mike1.2k
Jiang, Mike1.2k wrote:

Some flowJo gates stored in xml do not reflect the original boundaries.  So the gates need to be extended to include the events that the original gates meant enclose. There is no reliable way to tell when this should happen. So what the parser is doing is to compare the gate coordinates with an adjustable threshold 'extend_val and extend the gate to far left if it is below that threshold.

So to set 'extend_val' to -Inf is essentially disabling the extension, which may give you the wrong results when the extension is in fact expected.

Currently extension is implemented to rectangleGate and polygonGate, the reason you see the error from ellipse gate` is simply we were not sure what to do with ellipse extension (after all, extended ellipse will no longer be an ellipse). If you can send us the example workspace and FCS, we can certainly look at it and find the solution to it.

Gate extension details are also discussed here https://github.com/RGLab/flowWorkspace/issues/36

A bit late, but for anyone reading this, you should of course go with Mike's answer. Good insight in link.

I didn't see the effect on flowCore numbers as I always use the flowJo numbers for statistics.