#73: Expose abs argument at level of geom_stats

RGLab · Oct 28, 2020 · 0cdb186 · 0cdb186
1 parent 2596e7b
commit 0cdb186
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Showing 3 changed files with 15 additions and 6 deletions.
diff --git a/R/geom_stats.R b/R/geom_stats.R
@@ -7,7 +7,10 @@
 #' @param gate a 'filterList` or character (represent as a population node in GatingSet)
 #'             if not supplied, ggcyto then tries to parse the gate from the first geom_gate layer.
 #' @param negated whether the gate needs to be negated
-#' @param adjust adjust the position of the centroid. from 0 to 1.             
+#' @param adjust adjust the position of the centroid. from 0 to 1.
+#' @param abs If TRUE, the centroid will be calculated based on the full data range rather than
+#' the particular gate. This allows the adjust parameter to start from the center of the plot as opposed
+#' to the center of the gate.
 #' @param label.padding,label.size arguments passed to geom_label layer
 #' @param digits control the stats format
 #' @param ... other arguments passed to geom_label layer            
@@ -27,11 +30,11 @@
 #' # display gate name and percent
 #' p + geom_gate(c("CD4", "CD8")) + geom_stats(type = c("gate_name", "percent"))
 geom_stats <- function(gate = NULL, ..., value = NULL, type = "percent", negated = FALSE, adjust = 0.5
-                       , label.padding = unit(0.05, "lines"), label.size = 0, digits = 3){
+                       , abs = FALSE, label.padding = unit(0.05, "lines"), label.size = 0, digits = 3){
   type <- unlist(lapply(type, function(stat_type)match.arg(stat_type, c("percent", "count", "gate_name"))))
 
   structure(
-    list(gate = gate, value = value, type = type, negated = negated, adjust = adjust, digits = digits
+    list(gate = gate, value = value, type = type, negated = negated, adjust = adjust, abs = abs, digits = digits
          , geom_label_params = list(label.padding = label.padding
                                     , label.size = label.size
                                     , ...

diff --git a/R/ggcyto.R b/R/ggcyto.R
@@ -365,6 +365,7 @@ as.ggplot <- function(x, pre_binning = FALSE){
 
     negated <- e2[["negated"]]
     adjust <- e2[["adjust"]]
+    abs <- e2[["abs"]]
     digits <- e2[["digits"]]
     if(length(trans)>0)
     {
@@ -379,9 +380,12 @@ as.ggplot <- function(x, pre_binning = FALSE){
     for(gate in gates_parsed){
       if(length(trans)>0)
         gate <- transform(gate, translist)
-
-      #TODO: compute the actual data range from population data
-      abs <- is(gate[[1]], "booleanFilter")#bypass stats_postion computing by set abs to true to use data_range as gate_range(as a hack for now)
+
+      # Honor manual choice of abs == TRUE
+      if(!abs){
+        #TODO: compute the actual data range from population data
+        abs <- is(gate[[1]], "booleanFilter")#bypass stats_postion computing by set abs to true to use data_range as gate_range(as a hack for now) 
+      }
 
       stats <- compute_stats(fs, gate
                              , type = stat_type

diff --git a/R/ggcyto_GatingSet.R b/R/ggcyto_GatingSet.R
@@ -109,6 +109,7 @@ add_ggcyto_gs <- function(e1, e2){
 
   }else if(is(e2, "GeomStats")){
     adjust <- e2[["adjust"]]
+    abs <- e2[["abs"]]
 
     #grab the nodes info from previous gate layers
     nodes.geom_gate <- e1[["nodes"]]
@@ -149,6 +150,7 @@ add_ggcyto_gs <- function(e1, e2){
                                     , type = stat_type
                                     , negated = negated
                                     , adjust = adjust
+                                    , abs = abs
                                     , digits = digits
                                     )
                              , e2[["geom_label_params"]]