switching the [[ subsetting behavior for cytoset to returning a cytoframe by default

mikejiang commented 4 years ago

As mentioned in https://github.com/RGLab/flowWorkspace/issues/335#issuecomment-651372815, we will start the full transition of the reference paradigm for cytoset/cytoframe. i.e. cs[[i]] will return a cytoframe instead of flowFrame by default.

mikejiang commented 4 years ago

Now it returns a cytoframe by default

> cs
A cytoset with 2 samples.

  column names:
    FSC-A, FSC-H, FSC-W, SSC-A, B710-A, R660-A, R780-A, V450-A, V545-A, G560-A, G780-A, Time

> cs[[1]]
cytoframe object 'CytoTrol_CytoTrol_1.fcs'
with 119531 cells and 12 observables:
       name         desc  range minRange maxRange
$P1   FSC-A         <NA> 262143        0   262143
$P2   FSC-H         <NA> 262143        0   262143
...

To return a flowFrame


> cs[[1, returnType = "flowFrame"]]
flowFrame object 'CytoTrol_CytoTrol_1.fcs'
with 119531 cells and 12 observables:
       name         desc  range minRange maxRange
$P1   FSC-A         <NA> 262143        0   262143
$P2   FSC-H         <NA> 262143        0   262143
...

DillonHammill commented 4 years ago

Thanks @mikejiang! I will work on making the necessary changes to CytoExploreR. Thanks for updating fsApply as well.

RGLab / flowWorkspace

switching the [[ subsetting behavior for cytoset to returning a cytoframe by default #336