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close RGLab/flowWorkspace#212

Let's move the conversations here since we want to only keep the core infrastructural APIs at flowWorkspace and add the new peripheral helper functions in cytoUtils to ensure the former is stable.

@gfinak brought up an interesting idea of a general purpose API for computing population stats. I think it is worth to experiment to see how it works.

Hello, I hope someone can provide support.
I am trying to install cytoUtils using devtools and the command devtools::install_github("RGLab/cytoUtils")
but I receive the following error message:
`clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.2.0/lib/R/include" -DNDEBUG -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c cpPmden.cpp -o cpPmden.o
In file included from cpPmden.cpp:23:
./faust.h:3:10: fatal error: 'cpp11.hpp' file not found
#include <cpp11.hpp>
^~~~~~~~~~~
1 error generated.
make: *** [cpPmden.o] Error 1
ERROR: compilation failed for package ‘cytoUtils’

• removing ‘/Users/sp901610/.R/packages/420/cytoUtils’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/pf/d1qvdl8d1rg5h0lp9_fp4hd00000gp/T//RtmpAhxto3/filefde4397825a/cytoUtils_0.1.1.tar.gz’ had non-zero exit status`

it seems there is a missing file (cpp11.hpp) but I don't know how to solve it, could please someone help?

Many thanks

Hi guys,
I've experienced to process my longitudinal messy data on FlowJo. That's nightmare. I'm switching to openCyto. I'd like to input some suggestion on the potential features, which will be very beneficial for people if it can be implemented in Opencyto. For longitudinal data, when we generated the data at each time point, the setting of machine maybe slightly different.

1. The compensation definitely won't be identical in the first sample and the last one, if the study will last several years. So, the feature that individually compensated each sample based on it own compensation matrix will help data accuracy.
2. Actually, for some fluorochromes, they may have pretty similar/identical spectrum. In the flowjo, if one sample comes with AF488, the others is FITC, and we create the template based on AF488 and apply the template to all sample, then the samples with FITC channel cannot be plotted. Because flowjo considers they're two colors. But reality is, in practice, sometimes, when we setup machine, maybe we put AF488 in the channel instead of FITC (maybe for convenience or negligence et al, in our mind, the AF488 and FITC are almost the same). That brings the trouble when we look at the data. If Opencyto has this feature like automatically or semi-automatically check all samples' channel prior to heading to subsequent analysis, and make the consistency of the channels cross over all sample, that will be great helpful for handing "messy" data.

Thanks,
Joe

Hi

I tried installing the package from GitHub on Ubuntu, but got the following error along the way:

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘TreeSummarizedExperiment’

Installing TreeSummarizedExperiment allowed then allowed installation to succeed