add possibility to inverse.transform on gs_export_pop

functionsCyto.R

@@ -1,4 +1,4 @@
-gs_export_pop<-function(gs, pop, trim.channels=T){
+gs_export_pop<-function(gs, pop, trim.channels=T, inverse.transform=F){
   pop.dt<-c()
   # Initializes the progress bar
   pb <- txtProgressBar(min = 0,      # Minimum value of the progress bar
@@ -10,7 +10,7 @@ gs_export_pop<-function(gs, pop, trim.channels=T){
   
   for (i in 1:length(gs)){
     samp<-sampleNames(gs)[i]
-    data<-as.data.frame(flowCore::exprs(gh_pop_get_data(gs[[samp]], pop))) %>% add_column("Sample"=samp)
+    data<-as.data.frame(flowCore::exprs(gh_pop_get_data(gs[[samp]], pop, inverse.transform=inverse.transform))) %>% add_column("Sample"=samp)
     if (length(pop.dt) > 0){
       pop.dt<-rbind(pop.dt, data)
     }else{
@@ -71,7 +71,7 @@ transform_gs<-function(gs, saveparams=NULL, trans_params_obj=NULL, index=1){
   
   if (is.null(trans_params_obj)){
     log_mark<-colnames(gs)[!grepl("FS|SS|Time", colnames(gs))]
-    trans_params<-lapply(log_mark, function(x) list(channel=x, scale="biexp",maxvalue=250000,pos=4, widthBasis=-400, max=5, min=0))
+    trans_params<-lapply(log_mark, function(x) list(channel=x, scale="biexp",maxvalue=250000,pos=4, widthBasis=-400, max=10^3.7, min=0))
     names(trans_params)<-log_mark
     log_mark_lin<-colnames(gs)[grepl("FS|SS|Time", colnames(gs))]
     trans_params_lin<-lapply(log_mark_lin, function(x) list(channel=x, scale="lin", 
@@ -235,13 +235,14 @@ LMD2FCS<-function(files, output.dir=NULL){
 
 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){
+  pop_paths_full<-gs_get_pop_paths(gs)[gs_get_pop_paths(gs) != "root"]
+  if(!is.null(include)){pop_paths_full<-pop_paths_full[pop_paths_full %in% include]}
+  pop_paths<-lapply(pop_paths_full, function(x) rev(rev(strsplit(x, "/")[[1]])[1:2]))
+  for (gate.in in 1:length(pop_paths)){
+    gate<-pop_paths[[gate.in]]
     parent<-if (gate[1] == ""){"root"}else{gate[1]}
     gated_pop<-gate[2]
-    gates.list[[paste0(parent,"/",gated_pop)]]<-gs_pop_get_gate(gs, gated_pop)
+    gates.list[[paste0(parent,"/",gated_pop)]]<-gs_pop_get_gate(gs, pop_paths_full[gate.in])
   }
   if(save){saveRDS(gates.list, file)}
   return(gates.list)
@@ -283,9 +284,11 @@ gs_pop_get_children_recursive<-function(gs, pop){
 
 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])
+             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)
+  if (length(childrens)>0){
+    childrens_gate<-gates_save(gs, save=F, include=childrens) 
+  }
   
   gs_pop_add(gs, gs_pop_get_gate(gs, filterId), parent=subset, name="duplicated")
   
@@ -296,6 +299,7 @@ gs_gate_interactive_regate2<-function(gs, filterId, sample=1, subset="root", ...
                       dims = dims, regate=T, overlayGates = "duplicated")
   
   gs_pop_remove(gs, "duplicated")
-
-  gates_apply(gs, childrens_gate)
+  if (length(childrens)>0){
+    gates_apply(gs, childrens_gate)
+  }
 }