Adding functions gs_pop_get_children_recursive and gs_gate_interactive_regate2 and modifying gates_save by adding an "include" argument.

Analysis.R

@@ -40,7 +40,7 @@ gates[["NKdim"]]<-gs_pop_get_gate(gs, "NKdim")
 gs_gate_interactive(gs[["NKs-K562"]],
   subset = "NKdim",
   filterId = "CD107a+",
-  dims = list("CD107a", "CD56"), overlayGates = "CD107a+")
+  dims = list("CD107a", "CD56"))
 gates[["CD107a+"]]<-gs_pop_get_gate(gs, "CD107a+")
 
 gates<-gates_save(gs, file = "gates.rds")
@@ -102,3 +102,4 @@ ggsave("Analysis.jpg")
 
 save_gs(gs, "gs_analysis")
 gs<-load_gs("gs_analysis/")
+

functionsCyto.R

@@ -233,9 +233,10 @@ LMD2FCS<-function(files, output.dir=NULL){
   print("Conversión completada")
 }
 
-gates_save<-function(gs, file="gates.rds", save=T){
+gates_save<-function(gs, file="gates.rds", save=T, include=NULL){
   gates.list<-list()
   pop_paths<-gs_get_pop_paths(gs)[gs_get_pop_paths(gs) != "root"]
+  if(!is.null(include)){pop_paths<-pop_paths[pop_paths %in% include]}
   pop_paths<-lapply(pop_paths, function(x) rev(rev(strsplit(x, "/")[[1]])[1:2]))
   for (gate in pop_paths){
     parent<-if (gate[1] == ""){"root"}else{gate[1]}
@@ -265,3 +266,36 @@ gates_apply<-function(gs, gates, exact=T){
   recompute(gs)
   return(gs)
 }
+
+gs_pop_get_children_recursive<-function(gs, pop){
+  childrens<-c()
+  n<-0
+  childrens<-c(childrens, gs_pop_get_children(gs, pop))
+  while(n != length(childrens)){
+    n<-length(childrens)
+    for (i in 1:length(childrens)){
+      childrens<-c(childrens, gs_pop_get_children(gs, childrens[i]))
+    }
+    childrens<-unique(childrens)
+  }
+  return(childrens)
+}
+
+gs_gate_interactive_regate2<-function(gs, filterId, sample=1, subset="root", ...){
+  dims<-list(names(gs_pop_get_gate(gs, filterId)[[1]]@parameters)[1],
+              names(gs_pop_get_gate(gs, filterId)[[1]]@parameters)[2])
+  childrens<-gs_pop_get_children_recursive(gs, filterId)
+  childrens_gate<-gates_save(gs, save=F, include=childrens)
+  
+  gs_pop_add(gs, gs_pop_get_gate(gs, filterId), parent=subset, name="duplicated")
+  
+  gs_gate_interactive(gs,
+                      subset = subset,
+                      filterId = filterId,
+                      sample=sample,
+                      dims = dims, regate=T, overlayGates = "duplicated")
+  
+  gs_pop_remove(gs, "duplicated")
+
+  gates_apply(gs, childrens_gate)
+}