cyto_convert to collapse gating set

[rwbaer]

Briefly describe what you hope to achieve: I am attempting to automatically draw a quad gate based on all the samples in my gating set and add a node to the nodes I already created in CytoExploreR manually.

I had intended to use gate_quad_sequential() from the openCyto package and then gs_pop_add from the flowworkspace package.

Since gate_quad_sequential() requires a flow frame I tried to use cyto_convert from CytoExploreR to collapse the gating set into a single flow frame, but I seem to end up with an empty flow frame. Clearly, I'm doing something wrong. I was expecting the result to based on root node.

Any suggestions on how to approach such a task? What am I misunderstanding about cyto_convert?

Code fragment below

Outline the steps taken to attempt to reach this goal (paste code below):

• Include all data preparation steps where appropriate.

  
  > # =======================================================
  > # Automated approach to quad gate (capital letter gates)
  > # -------------------------------------------------------
  > # merge all samples into a single flowframe for autogating
  > frAll = cyto_convert(gsSamp, return = 'flowFrame')
  > summary(frAll)
      TIME_MSW TIME_LSW FSC-HEIGHT FSC-AREA FSC-WIDTH SSC-HEIGHT SSC-AREA
  Min.          NA       NA         NA       NA        NA         NA       NA
  1st Qu.       NA       NA         NA       NA        NA         NA       NA
  Median        NA       NA         NA       NA        NA         NA       NA
  Mean         NaN      NaN        NaN      NaN       NaN        NaN      NaN
  3rd Qu.       NA       NA         NA       NA        NA         NA       NA
  Max.          NA       NA         NA       NA        NA         NA       NA
      SSC-WIDTH FL2-AREA FL4-AREA
  Min.           NA       NA       NA
  1st Qu.        NA       NA       NA
  Median         NA       NA       NA
  Mean          NaN      NaN      NaN
  3rd Qu.        NA       NA       NA
  Max.           NA       NA       NA

summary(gsSamp) Length Class Mode 5 GatingSet S4

Produce a quad filter object

qg = gate_quad_sequential(frAll,

• channels = c("FL4-AREA", "FL2-AREA"),
• gFunc = mindensity,
• min = c(5e2, 5e2),
• max = c(1e6, 1e6)) Error in if (nrow(peaks) < 2) score <- 0 else score <- abs(diff(peaks[, : argument is of length zero In addition: Warning message: In .find_peaks(x, ..., num_peaks = 2) : At least 2 observations must be given in 'x' to find peaks.

  Turn the quad filter object into 4 gating nodes

  use capitalized gate names to stay unique

  gs_pop_add(gsSamp, gq, validityCheck = TRUE,

• names = c("Apoptotic", "Necrotic-Apoptotic", "Necrotic", "Live")) Error in is(gate, "filter") : object 'gq' not found

Include any associated screenshots or images here:

[DillonHammill]

cyto_convert() was originally designed for internal use only - in fact it has been removed from the new version of CytoExploreR. You should not attempt to gate data at the level of a cytoframe or cytoset, you should instead use cyto_gatingTemplate_edit() to add new openCyto entries to the gatingTemplate or call gs_add_gating_method() and update the gatingTemplate manually afterwards.

Remember, within CytoExploreR, the gatingTemplate serves as a means of keeping track of all the gating changes made to your GatingSet - it is important that any gates applied to your samples are accompanied with an entry in the gatingTemplate.

[rwbaer]

@DillonHammill With your help, I think I am now beginning to understand the philosophy behind integrating opencyto gates with cyto_explorer. This should open up more robust ways to analyze data. Your contributions have been really important. Thanks.