add multiple datasets support to read.ncdfFlowSet #47

RGLab · Jul 31, 2019 · 6d334c5 · 6d334c5
1 parent 050cdc6
commit 6d334c5
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Showing 2 changed files with 27 additions and 4 deletions.
diff --git a/R/ncdfIO.R b/R/ncdfIO.R
@@ -62,7 +62,7 @@ read.ncdfFlowSet <- function(files = NULL
 								,...) #dots to be passed to read.FCS
 {
     dots <- list(...)
-    emptyValue <- ifelse("emptyValue" %in% names(dots), dots[["emptyValue"]], TRUE)
+    dots[["emptyValue"]] <- ifelse("emptyValue" %in% names(dots), dots[["emptyValue"]], TRUE)
     dim <- as.integer(match.arg(as.character(dim), c("2","3")))
     channel_alias <- flowCore:::check_channel_alias(channel_alias)    
 
@@ -94,7 +94,10 @@ read.ncdfFlowSet <- function(files = NULL
     fileIds <- seq_len(nFile)
 
     getChnlEvt <- function(curFile){
-      txt <- read.FCSheader(curFile, emptyValue = emptyValue)[[1]]
+
+      thisCall <- quote(read.FCSheader(curFile))
+      thisCall <- as.call(c(as.list(thisCall),dots))
+      txt <- eval(thisCall)[[1]]
       nChannels <- as.integer(txt[["$PAR"]])
       channelNames <- unlist(lapply(1:nChannels,function(i)flowCore:::readFCSgetPar(txt,paste("$P",i,"N",sep=""))))
       channelNames<- unname(channelNames)
@@ -166,8 +169,10 @@ read.ncdfFlowSet <- function(files = NULL
 		}
 	}else
 	  chnls_common <- channels
-
-	tmp <- read.FCSheader(files[1], emptyValue = emptyValue)[[1]]
+
+  thisCall <- quote(read.FCSheader(files[1]))
+  thisCall <- as.call(c(as.list(thisCall),dots))
+  tmp <- eval(thisCall)[[1]]
 
     #make a dummy parameters slot for every frames to pass the validity check of flowSet class
 	#Note:This call will generate wrong params when chnls_common is less than original chnls

diff --git a/tests/testthat/test_IO.R b/tests/testthat/test_IO.R
@@ -1,4 +1,22 @@
 context("IO test")
+
+test_that("multi data segment", {
+  dataPath <- "~/rglab/workspace/flowCore/misc/"
+  filename  <- file.path(dataPath, "multi-datasegment.fcs")
+  skip_if_not(file.exists(filename))
+  expect_warning(fr <- read.ncdfFlowSet(filename)[[1]], "39 additional data")
+  expect_is(fr, "flowFrame")
+  expect_equal(nrow(fr), 1244)
+
+  fr <- read.ncdfFlowSet(filename, dataset = 1)[[1]]
+  expect_equal(nrow(fr), 1244)
+  expect_equal(colnames(fr)[10], "FL2-PL")
+
+  fr <- read.ncdfFlowSet(filename, dataset = 10)[[1]]
+  expect_equal(nrow(fr), 955)
+  expect_equal(colnames(fr)[10], "testPL")
+})
+
 test_that("read.ncdfFlowSet", {
 
   path <- system.file("extdata","compdata","data",package="flowCore")