From e8921d52c870f36a905bbe0c4cee0418c55797fe Mon Sep 17 00:00:00 2001
From: Kevin Ushey <kevinushey@gmail.com>
Date: Wed, 26 Mar 2014 11:58:46 -0700
Subject: [PATCH] Fix some small bugs that snuck into
 COMPASSContainerFromGatingSet, start optimizing re: #29

---
 R/GatingSetToCOMPASS.R               |  4 ++--
 R/GetThresholdedIntensities.R        |  9 ++++-----
 examples/GetThresholdedIntensities.R | 24 ++++++++++++++++++++++--
 man/GetThresholdedIntensities.Rd     | 24 ++++++++++++++++++++++--
 4 files changed, 50 insertions(+), 11 deletions(-)

diff --git a/R/GatingSetToCOMPASS.R b/R/GatingSetToCOMPASS.R
index f381372..71dd21a 100644
--- a/R/GatingSetToCOMPASS.R
+++ b/R/GatingSetToCOMPASS.R
@@ -283,11 +283,11 @@ COMPASSContainerFromGatingSet <- function(gs = NULL, node = NULL, filter.fun = N
         map <- map[markers, ]
       }
       message("We will map the following nodes to markers:")
-      kable(map)
+      kable(as.data.frame(map))
       
       
       # construct the map
-      mp <- map[, desc]
+      mp <- as.character(map[, desc])
       names(mp) <- map[, node]
       mp <- as.list(mp)
     }
diff --git a/R/GetThresholdedIntensities.R b/R/GetThresholdedIntensities.R
index 3b85ab3..b6cb31c 100644
--- a/R/GetThresholdedIntensities.R
+++ b/R/GetThresholdedIntensities.R
@@ -98,8 +98,7 @@ GetThresholdedIntensities <- function(gs, node, map) {
     
     ## Try to guess whether we should be pulling names from the 'desc'
     ## column or the 'name' column of the flowSets
-    dat <- flowWorkspace::getData(gs, use.exprs=FALSE)
-    ff <- get( objects(dat@frames)[[1]], envir=dat@frames )
+    ff <- flowWorkspace::getData(gs[[1]], use.exprs=FALSE)
     params <- parameters(ff)@data
     
     ## First, check for a perfect match using a basic regex
@@ -151,9 +150,9 @@ GetThresholdedIntensities <- function(gs, node, map) {
         } else {
           node_path <- file.path(path, cNode)
         }
-        gate <- flowWorkspace::getGate(x, node_path)
-        thresh <- gate@min
-        exprs[, expr_nms[i]][ exprs[, expr_nms[i]] < thresh ] <- 0
+        ## find out what cells didn't fall into the gate
+        ind <- !flowWorkspace::getIndices(x, node_path)
+        exprs[ind, expr_nms[i]] <- 0
       }
       exprs <- exprs[ rowSums(exprs) > 0, , drop=FALSE]
       return(exprs)
diff --git a/examples/GetThresholdedIntensities.R b/examples/GetThresholdedIntensities.R
index 2c75910..02cbef6 100644
--- a/examples/GetThresholdedIntensities.R
+++ b/examples/GetThresholdedIntensities.R
@@ -28,13 +28,25 @@ if (require(flowWorkspace)) {
   fs <- flowSet( lapply(data, flowFrame) )
   gs <- GatingSet(fs)
   
+  ## Add some dummy metadata
+  meta <- pData(gs)
+  meta$PTID <- 1:10
+  pData(gs) <- meta
+  
+  gate <- rectangleGate( list(TNFa=c(-Inf,Inf)))
+  add(gs, gate, parent="root", name="dummy")
+  
+  ## Add dummy gate
+  
   ## Make some gates, and apply them
   invisible(lapply(marker_names, function(marker) {
     .gate <- setNames( list( c( rexp(1, runif(1, 1E-5, 1E-3)), Inf) ), marker )
     gate <- rectangleGate(.gate=.gate)
-    add(gs, gate, parent="root", name=paste0(marker, "+"))
+    add(gs, gate, parent="dummy", name=paste0(marker, "+"))
   }))
   
+  recompute(gs)
+  
   ## Map node names to channel names
   map=list(
     "TNFa+"="TNFa",
@@ -44,7 +56,15 @@ if (require(flowWorkspace)) {
   )
   
   ## Pull out the data as a COMPASS-friendly dataset
-  output <- GetThresholdedIntensities(gs, "root", map)
+  node <- "dummy"
+  map <- map
+  system.time(
+    output <- GetThresholdedIntensities(gs, "dummy", map)
+  )
+  
+  system.time(
+    output <- COMPASSContainerFromGatingSet(gs, "dummy", individual_id="PTID", sample_id="name")
+  )
   str(output)
   
 }
diff --git a/man/GetThresholdedIntensities.Rd b/man/GetThresholdedIntensities.Rd
index 1cad982..467d37c 100644
--- a/man/GetThresholdedIntensities.Rd
+++ b/man/GetThresholdedIntensities.Rd
@@ -61,13 +61,25 @@ if (require(flowWorkspace)) {
   fs <- flowSet( lapply(data, flowFrame) )
   gs <- GatingSet(fs)
   
+  ## Add some dummy metadata
+  meta <- pData(gs)
+  meta$PTID <- 1:10
+  pData(gs) <- meta
+  
+  gate <- rectangleGate( list(TNFa=c(-Inf,Inf)))
+  add(gs, gate, parent="root", name="dummy")
+  
+  ## Add dummy gate
+  
   ## Make some gates, and apply them
   invisible(lapply(marker_names, function(marker) {
     .gate <- setNames( list( c( rexp(1, runif(1, 1E-5, 1E-3)), Inf) ), marker )
     gate <- rectangleGate(.gate=.gate)
-    add(gs, gate, parent="root", name=paste0(marker, "+"))
+    add(gs, gate, parent="dummy", name=paste0(marker, "+"))
   }))
   
+  recompute(gs)
+  
   ## Map node names to channel names
   map=list(
     "TNFa+"="TNFa",
@@ -77,7 +89,15 @@ if (require(flowWorkspace)) {
   )
   
   ## Pull out the data as a COMPASS-friendly dataset
-  output <- GetThresholdedIntensities(gs, "root", map)
+  node <- "dummy"
+  map <- map
+  system.time(
+    output <- GetThresholdedIntensities(gs, "dummy", map)
+  )
+  
+  system.time(
+    output <- COMPASSContainerFromGatingSet(gs, "dummy", individual_id="PTID", sample_id="name")
+  )
   str(output)
   
 }