To ease the process of replicating the existing (usually a manual one) gating schemes, this function populate an empty gating template with the 'alias', 'pop', 'parent' and 'dims' columns that exacted from an GatingHierarchy, and leave the other columns (e.g. `gating_method`) blank. So users can make changes to that template instead of writing from scratch.

gh_generate_template(gh)

Arguments

gh

a GatingHierarchy likely parsed from a xml workspace

Value

a gating template in data.frame format that requires further edition after output to csv

Examples

library(flowWorkspace)
#> As part of improvements to flowWorkspace, some behavior of #> GatingSet objects has changed. For details, please read the section #> titled "The cytoframe and cytoset classes" in the package vignette: #> #> vignette("flowWorkspace-Introduction", "flowWorkspace")
dataDir <- system.file("extdata",package="flowWorkspaceData") gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE)) gh_generate_template(gs[[1]])
#> alias pop parent dims #> 1 not debris + root FSC-A,SSC-A #> 2 singlets + /not debris FSC-A,FSC-H #> 3 CD3+ + /not debris/singlets <V450-A>,SSC-A #> 4 DPT + /not debris/singlets/CD3+ <B710-A>,<R780-A> #> 5 DNT + /not debris/singlets/CD3+ <B710-A>,<R780-A> #> 6 CD8 + /not debris/singlets/CD3+ <B710-A>,<R780-A> #> 7 CCR7- 45RA- + /not debris/singlets/CD3+/CD8 <G560-A>,<G780-A> #> 8 CCR7+ 45RA- + /not debris/singlets/CD3+/CD8 <G560-A>,<G780-A> #> 9 CCR7+ 45RA+ + /not debris/singlets/CD3+/CD8 <G560-A>,<G780-A> #> 10 CCR7- 45RA+ + /not debris/singlets/CD3+/CD8 <G560-A>,<G780-A> #> 11 38- DR- + /not debris/singlets/CD3+/CD8 <R660-A>,<V545-A> #> 12 38+ DR- + /not debris/singlets/CD3+/CD8 <R660-A>,<V545-A> #> 13 38+ DR+ + /not debris/singlets/CD3+/CD8 <R660-A>,<V545-A> #> 14 38- DR+ + /not debris/singlets/CD3+/CD8 <R660-A>,<V545-A> #> 15 CD4 + /not debris/singlets/CD3+ <B710-A>,<R780-A> #> 16 CCR7- 45RA- + /not debris/singlets/CD3+/CD4 <G560-A>,<G780-A> #> 17 CCR7+ 45RA- + /not debris/singlets/CD3+/CD4 <G560-A>,<G780-A> #> 18 CCR7+ 45RA+ + /not debris/singlets/CD3+/CD4 <G560-A>,<G780-A> #> 19 CCR7- 45RA+ + /not debris/singlets/CD3+/CD4 <G560-A>,<G780-A> #> 20 38- DR- + /not debris/singlets/CD3+/CD4 <R660-A>,<V545-A> #> 21 38+ DR- + /not debris/singlets/CD3+/CD4 <R660-A>,<V545-A> #> 22 38+ DR+ + /not debris/singlets/CD3+/CD4 <R660-A>,<V545-A> #> 23 38- DR+ + /not debris/singlets/CD3+/CD4 <R660-A>,<V545-A> #> gating_method gating_args collapseDataForGating groupBy preprocessing_method #> 1 <NA> <NA> <NA> <NA> <NA> #> 2 <NA> <NA> <NA> <NA> <NA> #> 3 <NA> <NA> <NA> <NA> <NA> #> 4 <NA> <NA> <NA> <NA> <NA> #> 5 <NA> <NA> <NA> <NA> <NA> #> 6 <NA> <NA> <NA> <NA> <NA> #> 7 <NA> <NA> <NA> <NA> <NA> #> 8 <NA> <NA> <NA> <NA> <NA> #> 9 <NA> <NA> <NA> <NA> <NA> #> 10 <NA> <NA> <NA> <NA> <NA> #> 11 <NA> <NA> <NA> <NA> <NA> #> 12 <NA> <NA> <NA> <NA> <NA> #> 13 <NA> <NA> <NA> <NA> <NA> #> 14 <NA> <NA> <NA> <NA> <NA> #> 15 <NA> <NA> <NA> <NA> <NA> #> 16 <NA> <NA> <NA> <NA> <NA> #> 17 <NA> <NA> <NA> <NA> <NA> #> 18 <NA> <NA> <NA> <NA> <NA> #> 19 <NA> <NA> <NA> <NA> <NA> #> 20 <NA> <NA> <NA> <NA> <NA> #> 21 <NA> <NA> <NA> <NA> <NA> #> 22 <NA> <NA> <NA> <NA> <NA> #> 23 <NA> <NA> <NA> <NA> <NA> #> preprocessing_args #> 1 <NA> #> 2 <NA> #> 3 <NA> #> 4 <NA> #> 5 <NA> #> 6 <NA> #> 7 <NA> #> 8 <NA> #> 9 <NA> #> 10 <NA> #> 11 <NA> #> 12 <NA> #> 13 <NA> #> 14 <NA> #> 15 <NA> #> 16 <NA> #> 17 <NA> #> 18 <NA> #> 19 <NA> #> 20 <NA> #> 21 <NA> #> 22 <NA> #> 23 <NA>