We assume the data is already compensated and transformed, but not scaled yet. The same scaling parameters as from the original grid will be used.
The code shows that if compensation/transform/scale slots are present in the flowSOM object those operations are applied to the flowframe.
https://github.com/SofieVG/FlowSOM/blob/50daac28a7c4da9ece429727f8143a015e965bcd/R/3_buildMST.R#L1794-L1811
I think the doc should be updated accordingly. The example should also be changed because a flowframe might be compensated and transformed twice currently leading to wrong interpretations.
Let me know if I should setup a PR. Best.
SamGG
commented
5 years ago
Hi. The doc states that
The code shows that if compensation/transform/scale slots are present in the flowSOM object those operations are applied to the flowframe. https://github.com/SofieVG/FlowSOM/blob/50daac28a7c4da9ece429727f8143a015e965bcd/R/3_buildMST.R#L1794-L1811 I think the doc should be updated accordingly. The example should also be changed because a flowframe might be compensated and transformed twice currently leading to wrong interpretations. Let me know if I should setup a PR. Best.