Nothing
tests/testthat/test-IO.R
In flowCore: flowCore: Basic structures for flow cytometry data
context("flowSet/flowFrame IO...")
# expectRes <- readRDS("tests/testthat/expectResults.rds")
fs <- GvHD[1:2]
expectPD <- pData(fs)
expectPD[["Patient"]] <- as.integer(as.vector(expectPD[["Patient"]]))
expectPD[["Visit"]] <- as.integer(expectPD[["Visit"]])
expectPD[["name"]] <- I(paste0(expectPD[["name"]], ".fcs"))
# rownames(expectPD) <- paste0(rownames(expectPD), ".fcs")
tmpdir <- tempfile()
write.flowSet(fs, tmpdir)
test_that("read.FCS -- column.pattern", {
tmp <- GvHD[[1]]
idx <- c(1,2)
tmp <- tmp[, idx]
tmpfile <- tempfile()
write.FCS(tmp, tmpfile)
tmp1 <- read.FCS(tmpfile, column.pattern = paste(colnames(tmp), collapse = "|"))
expect_equivalent(keyword(tmp1)[["$PAR"]], '2')
expect_equivalent(tmp@exprs, tmp1@exprs, tolerance = 3e-08)
})
test_that("duplicated channels", {
dataPath <- "~/rglab/workspace/flowCore/misc/"
filename <- file.path(dataPath, "duplicate_channel.fcs")
skip_if_not(file.exists(filename))
expect_output(expect_warning(fr <- read.FCS(filename), "disambiguate channels"))
expect_equal(colnames(fr)[3:4], c("FL1-H-1", "FL1-H-2"))
})
test_that("read.FCSheader--multi data segment", {
dataPath <- "~/rglab/workspace/flowCore/misc/"
filename <- file.path(dataPath, "multi-datasegment.fcs")
skip_if_not(file.exists(filename))
expect_warning(txt <- read.FCSheader(filename)[[1]], "39 additional data")
expect_equal(txt[['$TOT']], "1244")
txt <- read.FCSheader(filename, dataset = 1)[[1]]
expect_equal(txt[['$TOT']], "1244")
txt <- read.FCSheader(filename, dataset = 10)[[1]]
expect_equal(txt[['$TOT']], "955")
})
test_that("write.FCS--write correct $BEGINDATA",{
mat <- matrix(1:30,ncol = 3, dimnames = list(NULL, letters[1:3]))
fr <- flowFrame(mat)
#add a dummy keyword to fill the TEXT segment so that itself actual offset is subject to change
#once the computed $ENDSTEXT (i.e. '995') replaces the original the placeholder (i.e. '0')
keyword(fr)[["test"]] <- paste(rep(0,655), collapse = "")
tmp <- tempfile()
write.FCS(fr, tmp)
fr2 <- read.FCS(tmp)
expect_equivalent(exprs(fr), exprs(fr2))
})
test_that("read.flowSet", {
files <- list.files(tmpdir, pattern = "fcs")
#no phenoData supplied
fs1 <- read.flowSet(files, path = tmpdir)
expect_equivalent(pData(fs1), expectPD[, "name", drop = F])
anno <- list.files(tmpdir, pattern = "txt", full = T)
pd <- Biobase::read.AnnotatedDataFrame(anno)
pd[["name"]] <- I(paste0(pd[["name"]], ".fcs"))
#with phenoData supplied
suppressWarnings(fs1 <- read.flowSet(files, path = tmpdir, phenoData = pd))
expect_equal(pData(fs1), expectPD)
#pd without name
pData(pd)[["name"]] <- NULL
suppressWarnings(fs1 <- read.flowSet(files, path = tmpdir, phenoData = pd))
pData(fs1)[["name"]] <- I(pData(fs1)[["name"]])
pData(fs1)["FCS_File"] <- NULL
expect_equal(pData(fs1), expectPD)
#pd with wrong name
pd <- Biobase::read.AnnotatedDataFrame(anno)
pData(pd)[["name"]] <- paste0(pData(pd)[["name"]], "dummy")
suppressWarnings(fs1 <- read.flowSet(files, path = tmpdir, phenoData = pd))
pData(pd)["FCS_File"] <- NULL
expect_equal(pData(fs1), pData(pd))
#create duplicated folder
tmpdir1 <- tempfile()
suppressWarnings(write.flowSet(fs, tmpdir1))
#try to read both folders in
files <- list.files(tmpdir, pattern = "fcs", full = T)
files1 <- list.files(tmpdir1, pattern = "fcs", full = T)
fs2 <- read.flowSet(c(files, files1))
#check duplicates
sn <- basename(files)
sn1 <- paste0(sn, ".1")
expect_equal(sampleNames(fs2), c(sn, sn1))
})
test_that("phenoData<-", {
pd <- expectPD
# without name column
pd[["name"]] <- NULL
pData(fs) <- pd
n1 <- pData(fs)[["name"]]
n1 <- paste0(n1, ".fcs")
#name column is added
expect_equal(expectPD[["name"]], I(n1))
# name to be different from rownames
pd[["name"]] <- letters[1:2]
pData(fs) <- pd
expect_equal(pData(fs)[["name"]], pd[["name"]])
expect_equal(rownames(pData(fs)), rownames(expectPD))
})
test_that("test write.FCS", {
fcsfile <- system.file("extdata/CytoTrol_CytoTrol_1.fcs", package = "flowWorkspaceData")
fr <- read.FCS(fcsfile)
tmp <- tempfile()
#change desc col
pData(parameters(fr))[6, "desc"] <- "38"
# Write to file
tmp <- tempfile()
write.FCS(fr,tmp)
fr1 <- read.FCS(tmp)
expect_equivalent(markernames(fr1)[2], "38")
# When I read the file back in, the SPILL matrix appears to be malformed.
fr <- read.FCS(fcsfile)
expect_equal(keyword(fr)[["transformation"]], "applied")
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["NHLBI"]], digest(fr)) #TODO:try to reproduce the check error once upgrade R to 3.5
write.FCS(fr,tmp)
fr1 <- read.FCS(tmp)
keys <- keyword(fr)
keys[["$TOT"]] <- trimws(keys[["$TOT"]])
keys[c("$BEGINDATA", "$ENDDATA")] <- NULL
keys.new <- keyword(fr1)
keys.new[["FILENAME"]] <- "setToDummy"
expect_equal(keys.new[names(keys)], keys, tol = 6e-6)
expect_equivalent(exprs(fr), exprs(fr1))
#disable default linearize trans
fr_notrans <- read.FCS(fcsfile, transformation = FALSE)
expect_null(keyword(fr_notrans)[["transformation"]])
#flowCore_$PnR and transformation keywords should be absent now
#and there are should be no other difference in keywords between the two read
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr_notrans)))]
expect_equal(length(missing.keys), 25)
expect_true(all(grepl("(flowCore_\\$P)|(transformation)", missing.keys)))
#any the resulted write will produce no trans related keyword r
suppressWarnings(write.FCS(fr_notrans,tmp))
fr1 <- read.FCS(tmp, transformation = FALSE)
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr1)))]
expect_equal(length(missing.keys), 25)
expect_true(all(grepl("(flowCore_\\$P)|(transformation)", missing.keys)))
# when default linearize is enabled
fr1 <- read.FCS(tmp)
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr1)))]
expect_equal(length(missing.keys), 0)
#transform fr
fr.trans <- transform(fr_notrans, estimateLogicle(fr_notrans, markernames(fr_notrans)))
expect_equal(keyword(fr.trans)[["transformation"]], "custom")
#new keywords flowCore_$P* has been inserted
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr.trans)))]
expect_equal(length(missing.keys), 0)
suppressWarnings(write.FCS(fr.trans,tmp))
#these keywords remains even disable trans when read it back
fr1 <- read.FCS(tmp, transformation = FALSE)
expect_equal(keyword(fr1)[["transformation"]], "custom")
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr1)))]
expect_equal(length(missing.keys), 0)
#and transformation flag has no effect on read when it is already custom
fr1 <- read.FCS(tmp)
expect_equal(keyword(fr1)[["transformation"]], "custom")
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr1)))]
expect_equal(length(missing.keys), 0)
# test delimiter(\) escaping
keyword(fr)[["$DATE"]] <- "05\\JUN\\2012"
suppressWarnings(write.FCS(fr,tmp, delimiter = "\\"))
fr1 <- read.FCS(tmp, emptyValue = F)
keys.new <- keyword(fr1)
keys.new[["FILENAME"]] <- "setToDummy"
expect_equal(keys.new[["$DATE"]], "05\\JUN\\2012")
keys.new[["$DATE"]] <- keys[["$DATE"]]
expect_equal(keys.new[names(keys)], keys, tol = 6e-6)
expect_equivalent(exprs(fr), exprs(fr1))
# write it again to see if the existing double delimiter is handled properly
suppressWarnings(write.FCS(fr1,tmp, delimiter = "\\"))
fr1 <- read.FCS(tmp, emptyValue = F)
keys.new <- keyword(fr1)
keys.new[["FILENAME"]] <- "setToDummy"
expect_equal(keys.new[["$DATE"]], "05\\JUN\\2012")
keys.new[["$DATE"]] <- keys[["$DATE"]]
expect_equal(keys.new[names(keys)], keys, tol = 6e-6)
expect_equivalent(exprs(fr), exprs(fr1))
#test other delimiter
suppressWarnings(write.FCS(fr,tmp, delimiter = ";"))
fr1 <- read.FCS(tmp, emptyValue = F)
keys.new <- keyword(fr1)
keys.new[["FILENAME"]] <- "setToDummy"
expect_equal(keys.new[["$DATE"]], "05\\JUN\\2012")
keys.new[["$DATE"]] <- keys[["$DATE"]]
expect_equal(keys.new[names(keys)], keys, tol = 6e-6)
expect_equivalent(exprs(fr), exprs(fr1))
#test quadrual-delimiter string
keyword(fr)[["$DATE"]] <- "05||JUN||2012"
suppressWarnings(write.FCS(fr,tmp, delimiter = "|"))
fr1 <- read.FCS(tmp, emptyValue = F)
keys.new <- keyword(fr1)
keys.new[["FILENAME"]] <- "setToDummy"
expect_equal(keys.new[["$DATE"]], "05||JUN||2012")
keys.new[["$DATE"]] <- keys[["$DATE"]]
expect_equal(keys.new[names(keys)], keys, tol = 6e-6)
expect_equivalent(exprs(fr), exprs(fr1))
#when colmn.pattern is used to subset channels in read.FCS
#make sure the id in $Pn is set properly in write.FCS
fr_sub <- read.FCS(fcsfile, column.pattern = '-A')
tmp <- tempfile()
suppressWarnings(write.FCS(fr_sub , filename = tmp))
fr1 <- read.FCS(tmp)
expect_equal(pData(parameters(fr_sub))[["name"]], pData(parameters(fr1))[["name"]], check.attributes = FALSE)
expect_equal(pData(parameters(fr_sub))[["desc"]], pData(parameters(fr1))[["desc"]], check.attributes = FALSE)
})
test_that("write.FCS -- subsetted flowframe", {
tmpfile <- tempfile()
f1 = GvHD[[2]][,c(1:6,8)]
write.FCS(f1, tmpfile)
f2 <- read.FCS(tmpfile)
expect_equal(keyword(f2)[["$P8N"]], NULL)
expect_equal(nrow(f2), 3405)
expect_equal(ncol(f2), 7)
expect_equal(colnames(f2), colnames(f1))
expect_equal(markernames(f2), markernames(f1))
expect_equivalent(exprs(f1), exprs(f2), tol = 8e-7)
f1 <- GvHD[[1]][1:2, 4:6]
write.FCS(f1, tmpfile)
f2 <- read.FCS(tmpfile)
expect_equal(markernames(f1), markernames(f2))
#add test since GvHD's range slot is not consistent with PnR thus can't be tested for range()
fcsfile <- system.file("extdata/CytoTrol_CytoTrol_1.fcs", package = "flowWorkspaceData")
f1 = read.FCS(fcsfile)
f1 <- f1[,c(1:6,8)]
write.FCS(f1, tmpfile)
f2 <- read.FCS(tmpfile)
expect_equal(nrow(f2), nrow(f1))
expect_equal(ncol(f2), 7)
expect_equal(colnames(f2), colnames(f1))
expect_equal(markernames(f2), markernames(f1))
rng <- range(f1)
rng[2,] <- rng[2,] + 1
expect_equal(range(f2), rng)
})
test_that("write.FCS -- subsetted (by row) flowframe", {
tmp <- GvHD[[1]]
#subset by rows
exprs(tmp) <- exprs(tmp)[sample(1:nrow(exprs(tmp)), 1000), ]
expect_equal(keyword(tmp)[["$TOT"]], "3420")
#write to fcs
tmpfile <- tempfile()
suppressWarnings(write.FCS(tmp,tmpfile))
tmp <- read.FCS(tmpfile)
expect_equal(keyword(tmp)[["$TOT"]], "1000")
#read the text segment without parsing
con <- file(tmpfile, open="rb")
offsets <- readFCSheader(con)
seek(con, offsets["textstart"])
txt <- readBin(con,"raw", offsets["textend"]-offsets["textstart"]+1)
txt <- iconv(rawToChar(txt), "", "latin1", sub="byte")
#validity check on the keyword
#(make sure it is not duplicated since it may pass flowCore parser but fail the third-party software like flowJo)
expect_equal(length(grep("\\$TOT", strsplit(txt, split = "\\|")[[1]])), 1)
close(con)
})
test_that("write.FCS -- update channel and marker", {
inputFcs <- GvHD[[1]]
colnames(inputFcs)
markernames(inputFcs)
kwParName <- "$P3N"
kwParLabel <- "$P3S"
parName <- "FL1-H"
newName <- "newname"
newLabel <- "newLabel"
#update channel
colnames(inputFcs)[which(colnames(inputFcs) == parName)] <- newName
#update stain/marker
names(newLabel) <- newName
markernames(inputFcs) <- newLabel
#see updated data
colnames(inputFcs)
markernames(inputFcs)
#write fcs
tmpfile <- tempfile()
write.FCS(inputFcs, tmpfile)
tmp1 <- read.FCS(tmpfile)
expect_equal(colnames(inputFcs), colnames(tmp1))
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"]]), 4, tolerance = 3e-4)
})
test_that("write.FCS -- add new cols", {
tmp <- GvHD[[1]]
kf <- kmeansFilter("FSC-H"=c("Pop1","Pop2","Pop3"), filterId="myKmFilter")
fres <- filter(tmp, kf)
cols <- as.integer(fres@subSet)
cols <- matrix(cols, dimnames = list(NULL, "km"))
tmp <- fr_append_cols(tmp, cols)
tmpfile <- tempfile()
write.FCS(tmp, tmpfile)
tmp1 <- read.FCS(tmpfile)
expect_equivalent(tmp@exprs, tmp1@exprs, tolerance = 3e-08)
#set transformation flag and reload it to append flowCore_$PnRmax
keyword(tmp)[["transformation"]] <- "none"
write.FCS(tmp, tmpfile)
tmp <- read.FCS(tmpfile)
#append again to check whether it takes care of flowCore_$PnRmax
keyword(tmp)[["transformation"]] <- "custom"
colnames(cols) <- "km1"
tmp <- fr_append_cols(tmp, cols)
write.FCS(tmp, tmpfile)
tmp1 <- read.FCS(tmpfile)
expect_equal(keyword(tmp1)[["flowCore_$P10Rmax"]], "3")
expect_equivalent(tmp@exprs, tmp1@exprs, tolerance = 3e-08)
})
test_that("write.FCS -- reordered cols", {
tmp <- GvHD[[1]]
idx <- c(3,1,2)
tmp <- tmp[, idx]
tmpfile <- tempfile()
write.FCS(tmp, tmpfile)
tmp1 <- read.FCS(tmpfile)
pd <- parameters(tmp)
cn <- as.vector(pd[["name"]])
expect_equal(rownames(parameters(tmp1)), paste0("$P", 1:3))
expect_equivalent(keyword(tmp1)[paste0("BD$P", 1:3, "N")], keyword(tmp)[paste0("BD$P", idx, "N")])
expect_equivalent(tmp@exprs, tmp1@exprs, tolerance = 3e-08)
})
test_that("write.FCS -- handle umlaut characters", {
tmp <- GvHD[[1]]
keyword(tmp)[["FILENAME"]] <- "ΓΌ_umlaut"
tmpfile <- tempfile()
write.FCS(tmp, tmpfile)
tmp1 <- read.FCS(tmpfile)
expect_equivalent(tmp@exprs, tmp1@exprs, tolerance = 3e-08)
})
test_that("write.flowSet: test2", {
data(GvHD)
foo <- GvHD[1:2]
## now write out into files
outDir <- tempfile()
suppressWarnings(write.flowSet(foo, outDir))
expect_equal(dir(outDir), c("annotation.txt", "s5a01.fcs", "s5a02.fcs"))
outDir <- tempfile()
suppressWarnings(write.flowSet(foo, outDir, filename = c("a")))
expect_equal(dir(outDir), c("1_a.fcs", "2_a.fcs", "annotation.txt"))
outDir <- tempfile()
suppressWarnings(write.flowSet(foo, outDir, filename = c("a", "b")))
expect_equal(dir(outDir), c("a.fcs", "annotation.txt", "b.fcs"))
})
test_that("read.FCS: channel_alias", {
data(GvHD)
fr1 <- GvHD[[1]]
fr2 <- GvHD[[2]]
colnames(fr1)[c(3,5)] <- c("AL1-H", "AL3-H")
## now write out into files
fcs1 <- tempfile()
write.FCS(fr1, fcs1)
fcs2 <- tempfile()
write.FCS(fr2, fcs2)
expect_message(expect_error(fs <- read.flowSet(c(fcs1,fcs2))),regexp = "doesn't have the identical colnames")
#strict matching by full name
map <- data.frame(alias = c("FL1", "FL3"), channels = c("AL1-H, FL1-H", "FL3-H, AL3-H"))
fs <- read.flowSet(c(fcs1,fcs2), channel_alias = map)
expect_equal(colnames(fs)[c(3,5)], c("FL1", "FL3"))
#partial matching
map <- data.frame(alias = c("FL1", "FL3"), channels = c("AL1, FL1", "FL3, AL3"))
fs <- read.flowSet(c(fcs1,fcs2), channel_alias = map)
expect_equal(colnames(fs)[c(3,5)], c("FL1", "FL3"))
#case insensitive matching
map <- data.frame(alias = c("FL1", "FL3"), channels = c("al1, FL1", "fl3, AL3"))
fs <- read.flowSet(c(fcs1,fcs2), channel_alias = map)
expect_equal(colnames(fs)[c(3,5)], c("FL1", "FL3"))
#ambigous partial matching
map <- data.frame(alias = c("FL1", "FL3"), channels = c("l1, FL1", "fl3, AL3"))
expect_error(fs <- read.flowSet(c(fcs1,fcs2), channel_alias = map), "multiple entries")
outDir <- tempfile()
suppressWarnings(write.flowSet(fs, outDir, filename = c("a", "b")))
fs1 <- read.flowSet(files = c("a.fcs", "b.fcs"), path = outDir)
expect_equal(keyword(fs1[[1]])[["$P3N"]], "FL1")
#update spillover as well
fcsfile <- system.file("extdata/CytoTrol_CytoTrol_1.fcs", package = "flowWorkspaceData")
fr <- read.FCS(fcsfile, channel_alias = data.frame(alias = c("FL1", "FL3"), channels = c("B710-A", "R780-A")))
expect_equal(colnames(spillover(fr)[[1]]), colnames(fr)[5:11])
#validity check on possible multiple channels matching to the same alias within one FCS
fcsfile <- system.file("extdata/CytoTrol_CytoTrol_1.fcs", package = "flowWorkspaceData")
expect_output(expect_warning(fr <- read.FCS(fcsfile, channel_alias = data.frame(alias = c("FL1", "FL3"), channels = c("B710-A,V545", "R780-A"))), "channel_alias: Multiple channels from one FCS"))
})
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context("flowSet/flowFrame IO...")
# expectRes <- readRDS("tests/testthat/expectResults.rds")
fs <- GvHD[1:2]
expectPD <- pData(fs)
expectPD[["Patient"]] <- as.integer(as.vector(expectPD[["Patient"]]))
expectPD[["Visit"]] <- as.integer(expectPD[["Visit"]])
expectPD[["name"]] <- I(paste0(expectPD[["name"]], ".fcs"))
# rownames(expectPD) <- paste0(rownames(expectPD), ".fcs")
tmpdir <- tempfile()
write.flowSet(fs, tmpdir)
test_that("read.FCS -- column.pattern", {
tmp <- GvHD[[1]]
idx <- c(1,2)
tmp <- tmp[, idx]
tmpfile <- tempfile()
write.FCS(tmp, tmpfile)
tmp1 <- read.FCS(tmpfile, column.pattern = paste(colnames(tmp), collapse = "|"))
expect_equivalent(keyword(tmp1)[["$PAR"]], '2')
expect_equivalent(tmp@exprs, tmp1@exprs, tolerance = 3e-08)
})
test_that("duplicated channels", {
dataPath <- "~/rglab/workspace/flowCore/misc/"
filename <- file.path(dataPath, "duplicate_channel.fcs")
skip_if_not(file.exists(filename))
expect_output(expect_warning(fr <- read.FCS(filename), "disambiguate channels"))
expect_equal(colnames(fr)[3:4], c("FL1-H-1", "FL1-H-2"))
})
test_that("read.FCSheader--multi data segment", {
dataPath <- "~/rglab/workspace/flowCore/misc/"
filename <- file.path(dataPath, "multi-datasegment.fcs")
skip_if_not(file.exists(filename))
expect_warning(txt <- read.FCSheader(filename)[[1]], "39 additional data")
expect_equal(txt[['$TOT']], "1244")
txt <- read.FCSheader(filename, dataset = 1)[[1]]
expect_equal(txt[['$TOT']], "1244")
txt <- read.FCSheader(filename, dataset = 10)[[1]]
expect_equal(txt[['$TOT']], "955")
})
test_that("write.FCS--write correct $BEGINDATA",{
mat <- matrix(1:30,ncol = 3, dimnames = list(NULL, letters[1:3]))
fr <- flowFrame(mat)
#add a dummy keyword to fill the TEXT segment so that itself actual offset is subject to change
#once the computed $ENDSTEXT (i.e. '995') replaces the original the placeholder (i.e. '0')
keyword(fr)[["test"]] <- paste(rep(0,655), collapse = "")
tmp <- tempfile()
write.FCS(fr, tmp)
fr2 <- read.FCS(tmp)
expect_equivalent(exprs(fr), exprs(fr2))
})
test_that("read.flowSet", {
files <- list.files(tmpdir, pattern = "fcs")
#no phenoData supplied
fs1 <- read.flowSet(files, path = tmpdir)
expect_equivalent(pData(fs1), expectPD[, "name", drop = F])
anno <- list.files(tmpdir, pattern = "txt", full = T)
pd <- Biobase::read.AnnotatedDataFrame(anno)
pd[["name"]] <- I(paste0(pd[["name"]], ".fcs"))
#with phenoData supplied
suppressWarnings(fs1 <- read.flowSet(files, path = tmpdir, phenoData = pd))
expect_equal(pData(fs1), expectPD)
#pd without name
pData(pd)[["name"]] <- NULL
suppressWarnings(fs1 <- read.flowSet(files, path = tmpdir, phenoData = pd))
pData(fs1)[["name"]] <- I(pData(fs1)[["name"]])
pData(fs1)["FCS_File"] <- NULL
expect_equal(pData(fs1), expectPD)
#pd with wrong name
pd <- Biobase::read.AnnotatedDataFrame(anno)
pData(pd)[["name"]] <- paste0(pData(pd)[["name"]], "dummy")
suppressWarnings(fs1 <- read.flowSet(files, path = tmpdir, phenoData = pd))
pData(pd)["FCS_File"] <- NULL
expect_equal(pData(fs1), pData(pd))
#create duplicated folder
tmpdir1 <- tempfile()
suppressWarnings(write.flowSet(fs, tmpdir1))
#try to read both folders in
files <- list.files(tmpdir, pattern = "fcs", full = T)
files1 <- list.files(tmpdir1, pattern = "fcs", full = T)
fs2 <- read.flowSet(c(files, files1))
#check duplicates
sn <- basename(files)
sn1 <- paste0(sn, ".1")
expect_equal(sampleNames(fs2), c(sn, sn1))
})
test_that("phenoData<-", {
pd <- expectPD
# without name column
pd[["name"]] <- NULL
pData(fs) <- pd
n1 <- pData(fs)[["name"]]
n1 <- paste0(n1, ".fcs")
#name column is added
expect_equal(expectPD[["name"]], I(n1))
# name to be different from rownames
pd[["name"]] <- letters[1:2]
pData(fs) <- pd
expect_equal(pData(fs)[["name"]], pd[["name"]])
expect_equal(rownames(pData(fs)), rownames(expectPD))
})
test_that("test write.FCS", {
fcsfile <- system.file("extdata/CytoTrol_CytoTrol_1.fcs", package = "flowWorkspaceData")
fr <- read.FCS(fcsfile)
tmp <- tempfile()
#change desc col
pData(parameters(fr))[6, "desc"] <- "38"
# Write to file
tmp <- tempfile()
write.FCS(fr,tmp)
fr1 <- read.FCS(tmp)
expect_equivalent(markernames(fr1)[2], "38")
# When I read the file back in, the SPILL matrix appears to be malformed.
fr <- read.FCS(fcsfile)
expect_equal(keyword(fr)[["transformation"]], "applied")
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["NHLBI"]], digest(fr)) #TODO:try to reproduce the check error once upgrade R to 3.5
write.FCS(fr,tmp)
fr1 <- read.FCS(tmp)
keys <- keyword(fr)
keys[["$TOT"]] <- trimws(keys[["$TOT"]])
keys[c("$BEGINDATA", "$ENDDATA")] <- NULL
keys.new <- keyword(fr1)
keys.new[["FILENAME"]] <- "setToDummy"
expect_equal(keys.new[names(keys)], keys, tol = 6e-6)
expect_equivalent(exprs(fr), exprs(fr1))
#disable default linearize trans
fr_notrans <- read.FCS(fcsfile, transformation = FALSE)
expect_null(keyword(fr_notrans)[["transformation"]])
#flowCore_$PnR and transformation keywords should be absent now
#and there are should be no other difference in keywords between the two read
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr_notrans)))]
expect_equal(length(missing.keys), 25)
expect_true(all(grepl("(flowCore_\\$P)|(transformation)", missing.keys)))
#any the resulted write will produce no trans related keyword r
suppressWarnings(write.FCS(fr_notrans,tmp))
fr1 <- read.FCS(tmp, transformation = FALSE)
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr1)))]
expect_equal(length(missing.keys), 25)
expect_true(all(grepl("(flowCore_\\$P)|(transformation)", missing.keys)))
# when default linearize is enabled
fr1 <- read.FCS(tmp)
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr1)))]
expect_equal(length(missing.keys), 0)
#transform fr
fr.trans <- transform(fr_notrans, estimateLogicle(fr_notrans, markernames(fr_notrans)))
expect_equal(keyword(fr.trans)[["transformation"]], "custom")
#new keywords flowCore_$P* has been inserted
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr.trans)))]
expect_equal(length(missing.keys), 0)
suppressWarnings(write.FCS(fr.trans,tmp))
#these keywords remains even disable trans when read it back
fr1 <- read.FCS(tmp, transformation = FALSE)
expect_equal(keyword(fr1)[["transformation"]], "custom")
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr1)))]
expect_equal(length(missing.keys), 0)
#and transformation flag has no effect on read when it is already custom
fr1 <- read.FCS(tmp)
expect_equal(keyword(fr1)[["transformation"]], "custom")
missing.keys <- names(keys)[which(!names(keys) %in% names(keyword(fr1)))]
expect_equal(length(missing.keys), 0)
# test delimiter(\) escaping
keyword(fr)[["$DATE"]] <- "05\\JUN\\2012"
suppressWarnings(write.FCS(fr,tmp, delimiter = "\\"))
fr1 <- read.FCS(tmp, emptyValue = F)
keys.new <- keyword(fr1)
keys.new[["FILENAME"]] <- "setToDummy"
expect_equal(keys.new[["$DATE"]], "05\\JUN\\2012")
keys.new[["$DATE"]] <- keys[["$DATE"]]
expect_equal(keys.new[names(keys)], keys, tol = 6e-6)
expect_equivalent(exprs(fr), exprs(fr1))
# write it again to see if the existing double delimiter is handled properly
suppressWarnings(write.FCS(fr1,tmp, delimiter = "\\"))
fr1 <- read.FCS(tmp, emptyValue = F)
keys.new <- keyword(fr1)
keys.new[["FILENAME"]] <- "setToDummy"
expect_equal(keys.new[["$DATE"]], "05\\JUN\\2012")
keys.new[["$DATE"]] <- keys[["$DATE"]]
expect_equal(keys.new[names(keys)], keys, tol = 6e-6)
expect_equivalent(exprs(fr), exprs(fr1))
#test other delimiter
suppressWarnings(write.FCS(fr,tmp, delimiter = ";"))
fr1 <- read.FCS(tmp, emptyValue = F)
keys.new <- keyword(fr1)
keys.new[["FILENAME"]] <- "setToDummy"
expect_equal(keys.new[["$DATE"]], "05\\JUN\\2012")
keys.new[["$DATE"]] <- keys[["$DATE"]]
expect_equal(keys.new[names(keys)], keys, tol = 6e-6)
expect_equivalent(exprs(fr), exprs(fr1))
#test quadrual-delimiter string
keyword(fr)[["$DATE"]] <- "05||JUN||2012"
suppressWarnings(write.FCS(fr,tmp, delimiter = "|"))
fr1 <- read.FCS(tmp, emptyValue = F)
keys.new <- keyword(fr1)
keys.new[["FILENAME"]] <- "setToDummy"
expect_equal(keys.new[["$DATE"]], "05||JUN||2012")
keys.new[["$DATE"]] <- keys[["$DATE"]]
expect_equal(keys.new[names(keys)], keys, tol = 6e-6)
expect_equivalent(exprs(fr), exprs(fr1))
#when colmn.pattern is used to subset channels in read.FCS
#make sure the id in $Pn is set properly in write.FCS
fr_sub <- read.FCS(fcsfile, column.pattern = '-A')
tmp <- tempfile()
suppressWarnings(write.FCS(fr_sub , filename = tmp))
fr1 <- read.FCS(tmp)
expect_equal(pData(parameters(fr_sub))[["name"]], pData(parameters(fr1))[["name"]], check.attributes = FALSE)
expect_equal(pData(parameters(fr_sub))[["desc"]], pData(parameters(fr1))[["desc"]], check.attributes = FALSE)
})
test_that("write.FCS -- subsetted flowframe", {
tmpfile <- tempfile()
f1 = GvHD[[2]][,c(1:6,8)]
write.FCS(f1, tmpfile)
f2 <- read.FCS(tmpfile)
expect_equal(keyword(f2)[["$P8N"]], NULL)
expect_equal(nrow(f2), 3405)
expect_equal(ncol(f2), 7)
expect_equal(colnames(f2), colnames(f1))
expect_equal(markernames(f2), markernames(f1))
expect_equivalent(exprs(f1), exprs(f2), tol = 8e-7)
f1 <- GvHD[[1]][1:2, 4:6]
write.FCS(f1, tmpfile)
f2 <- read.FCS(tmpfile)
expect_equal(markernames(f1), markernames(f2))
#add test since GvHD's range slot is not consistent with PnR thus can't be tested for range()
fcsfile <- system.file("extdata/CytoTrol_CytoTrol_1.fcs", package = "flowWorkspaceData")
f1 = read.FCS(fcsfile)
f1 <- f1[,c(1:6,8)]
write.FCS(f1, tmpfile)
f2 <- read.FCS(tmpfile)
expect_equal(nrow(f2), nrow(f1))
expect_equal(ncol(f2), 7)
expect_equal(colnames(f2), colnames(f1))
expect_equal(markernames(f2), markernames(f1))
rng <- range(f1)
rng[2,] <- rng[2,] + 1
expect_equal(range(f2), rng)
})
test_that("write.FCS -- subsetted (by row) flowframe", {
tmp <- GvHD[[1]]
#subset by rows
exprs(tmp) <- exprs(tmp)[sample(1:nrow(exprs(tmp)), 1000), ]
expect_equal(keyword(tmp)[["$TOT"]], "3420")
#write to fcs
tmpfile <- tempfile()
suppressWarnings(write.FCS(tmp,tmpfile))
tmp <- read.FCS(tmpfile)
expect_equal(keyword(tmp)[["$TOT"]], "1000")
#read the text segment without parsing
con <- file(tmpfile, open="rb")
offsets <- readFCSheader(con)
seek(con, offsets["textstart"])
txt <- readBin(con,"raw", offsets["textend"]-offsets["textstart"]+1)
txt <- iconv(rawToChar(txt), "", "latin1", sub="byte")
#validity check on the keyword
#(make sure it is not duplicated since it may pass flowCore parser but fail the third-party software like flowJo)
expect_equal(length(grep("\\$TOT", strsplit(txt, split = "\\|")[[1]])), 1)
close(con)
})
test_that("write.FCS -- update channel and marker", {
inputFcs <- GvHD[[1]]
colnames(inputFcs)
markernames(inputFcs)
kwParName <- "$P3N"
kwParLabel <- "$P3S"
parName <- "FL1-H"
newName <- "newname"
newLabel <- "newLabel"
#update channel
colnames(inputFcs)[which(colnames(inputFcs) == parName)] <- newName
#update stain/marker
names(newLabel) <- newName
markernames(inputFcs) <- newLabel
#see updated data
colnames(inputFcs)
markernames(inputFcs)
#write fcs
tmpfile <- tempfile()
write.FCS(inputFcs, tmpfile)
tmp1 <- read.FCS(tmpfile)
expect_equal(colnames(inputFcs), colnames(tmp1))
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"]]), 4, tolerance = 3e-4)
})
test_that("write.FCS -- add new cols", {
tmp <- GvHD[[1]]
kf <- kmeansFilter("FSC-H"=c("Pop1","Pop2","Pop3"), filterId="myKmFilter")
fres <- filter(tmp, kf)
cols <- as.integer(fres@subSet)
cols <- matrix(cols, dimnames = list(NULL, "km"))
tmp <- fr_append_cols(tmp, cols)
tmpfile <- tempfile()
write.FCS(tmp, tmpfile)
tmp1 <- read.FCS(tmpfile)
expect_equivalent(tmp@exprs, tmp1@exprs, tolerance = 3e-08)
#set transformation flag and reload it to append flowCore_$PnRmax
keyword(tmp)[["transformation"]] <- "none"
write.FCS(tmp, tmpfile)
tmp <- read.FCS(tmpfile)
#append again to check whether it takes care of flowCore_$PnRmax
keyword(tmp)[["transformation"]] <- "custom"
colnames(cols) <- "km1"
tmp <- fr_append_cols(tmp, cols)
write.FCS(tmp, tmpfile)
tmp1 <- read.FCS(tmpfile)
expect_equal(keyword(tmp1)[["flowCore_$P10Rmax"]], "3")
expect_equivalent(tmp@exprs, tmp1@exprs, tolerance = 3e-08)
})
test_that("write.FCS -- reordered cols", {
tmp <- GvHD[[1]]
idx <- c(3,1,2)
tmp <- tmp[, idx]
tmpfile <- tempfile()
write.FCS(tmp, tmpfile)
tmp1 <- read.FCS(tmpfile)
pd <- parameters(tmp)
cn <- as.vector(pd[["name"]])
expect_equal(rownames(parameters(tmp1)), paste0("$P", 1:3))
expect_equivalent(keyword(tmp1)[paste0("BD$P", 1:3, "N")], keyword(tmp)[paste0("BD$P", idx, "N")])
expect_equivalent(tmp@exprs, tmp1@exprs, tolerance = 3e-08)
})
test_that("write.FCS -- handle umlaut characters", {
tmp <- GvHD[[1]]
keyword(tmp)[["FILENAME"]] <- "ΓΌ_umlaut"
tmpfile <- tempfile()
write.FCS(tmp, tmpfile)
tmp1 <- read.FCS(tmpfile)
expect_equivalent(tmp@exprs, tmp1@exprs, tolerance = 3e-08)
})
test_that("write.flowSet: test2", {
data(GvHD)
foo <- GvHD[1:2]
## now write out into files
outDir <- tempfile()
suppressWarnings(write.flowSet(foo, outDir))
expect_equal(dir(outDir), c("annotation.txt", "s5a01.fcs", "s5a02.fcs"))
outDir <- tempfile()
suppressWarnings(write.flowSet(foo, outDir, filename = c("a")))
expect_equal(dir(outDir), c("1_a.fcs", "2_a.fcs", "annotation.txt"))
outDir <- tempfile()
suppressWarnings(write.flowSet(foo, outDir, filename = c("a", "b")))
expect_equal(dir(outDir), c("a.fcs", "annotation.txt", "b.fcs"))
})
test_that("read.FCS: channel_alias", {
data(GvHD)
fr1 <- GvHD[[1]]
fr2 <- GvHD[[2]]
colnames(fr1)[c(3,5)] <- c("AL1-H", "AL3-H")
## now write out into files
fcs1 <- tempfile()
write.FCS(fr1, fcs1)
fcs2 <- tempfile()
write.FCS(fr2, fcs2)
expect_message(expect_error(fs <- read.flowSet(c(fcs1,fcs2))),regexp = "doesn't have the identical colnames")
#strict matching by full name
map <- data.frame(alias = c("FL1", "FL3"), channels = c("AL1-H, FL1-H", "FL3-H, AL3-H"))
fs <- read.flowSet(c(fcs1,fcs2), channel_alias = map)
expect_equal(colnames(fs)[c(3,5)], c("FL1", "FL3"))
#partial matching
map <- data.frame(alias = c("FL1", "FL3"), channels = c("AL1, FL1", "FL3, AL3"))
fs <- read.flowSet(c(fcs1,fcs2), channel_alias = map)
expect_equal(colnames(fs)[c(3,5)], c("FL1", "FL3"))
#case insensitive matching
map <- data.frame(alias = c("FL1", "FL3"), channels = c("al1, FL1", "fl3, AL3"))
fs <- read.flowSet(c(fcs1,fcs2), channel_alias = map)
expect_equal(colnames(fs)[c(3,5)], c("FL1", "FL3"))
#ambigous partial matching
map <- data.frame(alias = c("FL1", "FL3"), channels = c("l1, FL1", "fl3, AL3"))
expect_error(fs <- read.flowSet(c(fcs1,fcs2), channel_alias = map), "multiple entries")
outDir <- tempfile()
suppressWarnings(write.flowSet(fs, outDir, filename = c("a", "b")))
fs1 <- read.flowSet(files = c("a.fcs", "b.fcs"), path = outDir)
expect_equal(keyword(fs1[[1]])[["$P3N"]], "FL1")
#update spillover as well
fcsfile <- system.file("extdata/CytoTrol_CytoTrol_1.fcs", package = "flowWorkspaceData")
fr <- read.FCS(fcsfile, channel_alias = data.frame(alias = c("FL1", "FL3"), channels = c("B710-A", "R780-A")))
expect_equal(colnames(spillover(fr)[[1]]), colnames(fr)[5:11])
#validity check on possible multiple channels matching to the same alias within one FCS
fcsfile <- system.file("extdata/CytoTrol_CytoTrol_1.fcs", package = "flowWorkspaceData")
expect_output(expect_warning(fr <- read.FCS(fcsfile, channel_alias = data.frame(alias = c("FL1", "FL3"), channels = c("B710-A,V545", "R780-A"))), "channel_alias: Multiple channels from one FCS"))
})
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