From 6cc1fccb975235c297f529556c157fd0ebd7b2b1 Mon Sep 17 00:00:00 2001
From: mikejiang <wjiang2@fhcrc.org>
Date: Fri, 24 Aug 2018 14:51:27 -0700
Subject: [PATCH] use the actual range instead of 1024 for  in write.FCS #122

---
 NAMESPACE                             |  2 +-
 R/IO.R                                | 11 +++++++----
 tests/testthat/helper-expectResults.R |  1 +
 tests/testthat/test-IO.R              | 12 ++++++++++++
 tests/testthat/test-fr-methods.R      |  1 +
 5 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 0bd6502..42f1683 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,7 +2,7 @@ useDynLib("flowCore",.registration=TRUE)
 
 import(methods)
 import(Rcpp)
-importFrom(matrixStats, colMins)
+importFrom(matrixStats, colMins, colMaxs)
 importClassesFrom(Biobase, AnnotatedDataFrame)
 importFrom("grDevices", "devAskNewPage")
   importFrom("graphics", "abline")
diff --git a/R/IO.R b/R/IO.R
index bb09697..c526324 100644
--- a/R/IO.R
+++ b/R/IO.R
@@ -1391,10 +1391,13 @@ write.FCS <- function(x, filename, what="numeric", delimiter = "|", endian = "bi
     pne[sapply(pne, length)==0] <- "0,0"
     mk <- c(mk, pne)
     
-    ## The same for PnR, "1024" if missing
+    mat <- exprs(x)
+    ## The same for PnR, 
     pnr <- orig.kw[paste0(pid, "R")]
     names(pnr) <- sprintf("$P%sR", newid)
-    pnr[sapply(pnr, length)==0] <- "1024"
+    empty_range_ind <- sapply(pnr, length)==0
+    empty_range_chnl <- as.character(pd[pid[empty_range_ind],"name"])
+    pnr[empty_range_ind] <- colMaxs(mat[, empty_range_chnl, drop = FALSE])
     mk <- c(mk, pnr)
     
     ## Now update the PnN keyword
@@ -1415,7 +1418,7 @@ write.FCS <- function(x, filename, what="numeric", delimiter = "|", endian = "bi
     description(x) <- mk
     
     ## Figure out the offsets based on the size of the initial text section
-    ld <-  length(exprs(x)) * types[what, "bitwidth"]
+    ld <-  length(mat) * types[what, "bitwidth"]
     ctxt <- collapseDesc(x, delimiter = delimiter)
     
     # these two are estimated value and just to get the reserved length of characters for storing the
@@ -1437,7 +1440,7 @@ write.FCS <- function(x, filename, what="numeric", delimiter = "|", endian = "bi
     on.exit(close(con))
     writeFCSheader(con, offsets)
     writeChar(ctxt, con, eos=NULL)
-    writeBin(as(t(exprs(x)), what), con, size=types[what, "bitwidth"],
+    writeBin(as(t(mat), what), con, size=types[what, "bitwidth"],
              endian=endian)
 	writeChar("00000000", con, eos=NULL)
     filename
diff --git a/tests/testthat/helper-expectResults.R b/tests/testthat/helper-expectResults.R
index ac3a939..aea622b 100644
--- a/tests/testthat/helper-expectResults.R
+++ b/tests/testthat/helper-expectResults.R
@@ -1,3 +1,4 @@
 library(digest)
+library(Biobase)
 expectRes <- readRDS("expectResults.rds")
 data(GvHD)
diff --git a/tests/testthat/test-IO.R b/tests/testthat/test-IO.R
index c947546..8ac147d 100644
--- a/tests/testthat/test-IO.R
+++ b/tests/testthat/test-IO.R
@@ -265,6 +265,18 @@ test_that("write.FCS -- update channel and marker", {
   expect_equal(markernames(inputFcs), markernames(tmp1))
 })
 
+test_that("write.FCS -- data from the flowFrame constructor without $PnR keys", {
+  set.seed(1)
+  mat <- matrix(rnorm(1000),ncol=4)
+  colnames(mat) <- LETTERS[1:4]
+  fr1 <- flowFrame(mat)
+  keyword(fr1)
+  tmp <- tempfile()
+  write.FCS(fr1, tmp)
+  fr2 <- read.FCS(tmp)
+  expect_equal(as.numeric(keyword(fr2)[["$P1R"]]), 2.4977, tolerance = 3e-4)
+})
+
 test_that("write.FCS -- add new cols", {
   tmp <- GvHD[[1]]
   
diff --git a/tests/testthat/test-fr-methods.R b/tests/testthat/test-fr-methods.R
index 836c4ba..cb851bc 100644
--- a/tests/testthat/test-fr-methods.R
+++ b/tests/testthat/test-fr-methods.R
@@ -1,6 +1,7 @@
 context("flowFrame methods...")
 data("GvHD")
 fr <- GvHD[[1]]
+
 test_that("range", {
   rng1 <- data.frame("FSC-H" = c(0,1023)
                      ,"SSC-H" = c(0,1023)