Commit made by the Bioconductor Git-SVN bridge.

Consists of 2 commit(s).

Commit information:

    Commit id: e8921d5
    Commit message:
    Fix some small bugs that snuck into COMPASSContainerFromGatingSet, start optimizing re: #29
    Committed by Kevin Ushey <kevinushey at gmail.com>
    Commit date: 2014-03-26T11:58:46-07:00

    Commit id: 1bbd026
    Commit message:
    Merge branch 'master' of https://github.com/RGLab/COMPASS
    Committed by Kevin Ushey <kevinushey at gmail.com>
    Commit date: 2014-03-26T11:58:55-07:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COMPASS@87956 bc3139a8-67e5-0310-9ffc-ced21a209358

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)
     }

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)

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)
 
 }

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)
 
 }