tests/testthat/IO-testSuite.R
In RGLab/flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.
context("Functional Tests Related to Loading/Saving cytoframes from FCS")
# adapted from flowCore IO-testSuite.R
library(digest)
dataPath <- "~/rglab/workspace/flowCore/misc/"
expectRes <- readRDS("~/rglab/workspace/flowCore/tests/testthat/expectResults.rds")
expectRes.new <- readRDS("~/rglab/workspace/flowCore/tests/testthat/expectRes.new.rds")
# NOTE: These tests are adapted for load_cytoframe_from_fcs() with as few changes as possible from the I/O tests for
# read.FCS() from flowCore's IO-testSuite.R. Where a test was changed due to expected changes in behavior
# between cytoframe and flowFrame or between load_cytoframe_from_fcs() and read.FCS(), those were indicated
# with "CHANGE". Many tests will require further adaptation (particularly those relying on digest()), so
# this is a work in progress. All comments (and commented-out lines) were left intact.
# saveRDS(expectRes.new, file = "~/rglab/workspace/flowCore/tests/testthat/expectRes.new.rds")
# test_that("Miltenyi's Macsquantify", {
# expect_warning(
# fr <- read.FCS(file.path(dataPath, "Miltenyi/1696_12017-04-30.0001_compatible.fcs"))
# , "Missing the required")
# expect_is(fr, "flowFrame")
#
# range(fr, type = "data")
# range(fr)
# expect_warning(fr <- read.FCS(file.path(dataPath, "double_precision/wishbone_thymus_panel1_rep1.fcs")), "Missing the required")
#
# expect_equal(nrow(fr), 250170)
#
# })
# expectRes.new <- list()
test_that("big file", {
#too slow to run
# fr <- read.FCS(file.path(dataPath, "gigantic_file.fcs"), column.pattern = "FSC*")
# CHANGE -- cytoset errors out for this, while trunk does not
fr <- expect_error(load_cytoframe_from_fcs(file.path(dataPath, "gigantic_file.fcs")
, which.lines = c(1,1e9)
, column.pattern = "FSC*"), "which.lines exceeds the data boundary")
# expect_equal(nrow(fr), 1)
fr <- load_cytoframe_from_fcs(file.path(dataPath, "gigantic_file.fcs"), which.lines = 1:1e3)
expect_equal(nrow(fr), 1e3)
fr <- load_cytoframe_from_fcs(file.path(dataPath, "gigantic_file.fcs"), which.lines = (1e3+1):2e3)
expect_equal(nrow(fr), 1e3)
})
# CHANGE: warnings are just console output for now. So all "expect_warning" calls are now "expect_output".
test_that("DATATYPE:'D'", {
expect_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, "double_precision/wishbone_myleoid_monocyte.fcs")), "warning:Missing the required")
expect_is(fr, "cytoframe")
filename <- "wishbone_thymus_panel1_rep1.fcs"
msg <- capture_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, "double_precision", filename)))
expect_match(msg, "Missing the required")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
expect_equal(nrow(fr), 250170)
})
test_that("multi data segment", {
expect_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, "multi-datasegment.fcs")), "additional data segment")
expect_is(fr, "cytoframe")
expect_equal(nrow(fr), 1244)
filename <- "multi-datasegment.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename), dataset = 1)
expect_equal(nrow(fr), 1244)
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename), dataset = 10)
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
expect_equal(nrow(fr), 955)
})
test_that("FCS with both SPILL and $SPILLOVER present", {
filename <- "example-spill-spillover.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
expect_equal(keyword(fr)[["SPILL"]], keyword(fr)[["$SPILLOVER"]])
# CHANGE: spillover() now will allow direct specfication of keyword, but only returns single matrix
tmp1 <- spillover(fr)
tmp2 <- spillover(fr, "$SPILLOVER")
expect_equal(tmp1, tmp2)
tmp <- tempfile()
write.FCS(fr, filename = tmp)
fr <- load_cytoframe_from_fcs(tmp)
expect_equal(keyword(fr)[["SPILL"]], keyword(fr)[["$SPILLOVER"]])
})
test_that("test uint_64 + diverse bitwidths + missing $NEXTDATA: '*' ", {
filename <- "uint_64.lxb"
# CHANGE: This warning is not implemented in load_cytoframe_from_fcs as it is in read.FCS.
# If '$PnE' not found, just defaults to '0,0' silently. Leaving the check in for now, but failure is expected.
expect_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, filename)), "No '$PnE' keyword")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
})
#TODO: investigate why the results is no longer consistent with the archived summary
test_that("mixed endian", {
filename <- "mixedEndian.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
expect_is(fr, "cytoframe")
# expect_equal(summary(fr), expectRes[["read.FCS"]][["mixedEndian"]])
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
})
# 'FILENAME' keyword may change when file path is changed
# so we hard code it to make the comparsion consistent in case the file is moved
test_that("test special delimiter character: '*' ", {
filename <- "multi_data_segment.LMD"
expect_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, filename)), "additional data segment")
expect_equal(summary(fr), expectRes[["read.FCS"]][["multi_data_segment"]], tolerance = 0.08)
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
})
test_that("test special delimiter character: '*' ", {
filename <- "specialDelimiter.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
expect_equal(summary(fr), expectRes[["read.FCS"]][["specialDelimiter"]], tolerance = 0.001)
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
})
test_that("test flowJo exported data with missing some of PnR keywords ", {
expect_output(expect_error(fr <- load_cytoframe_from_fcs(file.path(dataPath, "missing_PnR_flowJoExport.fcs"))
, "not contained"), "warning:Missing the required \\$BEGINDATA keyword")
})
test_that("test in consistent datastart between header and TEXT", {
expect_output(expect_error(fr <- load_cytoframe_from_fcs(file.path(dataPath, "Accuri-C6", "Accuri - C6 - A02 Spherotech 8 Peak Beads.fcs"), emptyValue = FALSE)
, "HEADER and the TEXT")
, "uneven number of tokens")
filename <- "Accuri - C6 - A02 Spherotech 8 Peak Beads.fcs"
msg <- capture_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, "Accuri-C6", filename), emptyValue = FALSE, ignore.text.offset = TRUE))
expect_match(msg, "HEADER and the TEXT")
expect_match(msg, "uneven number of tokens")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
expect_equal(nrow(fr), 60661)
expect_equal(summary(fr), expectRes[["read.FCS"]][["Accuri-C6"]], tolerance = 0.001)
msg <- capture_output(fs <- load_cytoset_from_fcs(file.path(dataPath, "Accuri-C6", filename), emptyValue = FALSE, ignore.text.offset = TRUE))
expect_match(msg, "HEADER and the TEXT")
expect_match(msg, "uneven number of tokens")
expect_equal(nrow(fs[[1]]), 60661)
})
# CHANGE: C parser errors on odd bitwidth, so disable tests subsequent to parse attempt.
test_that("test odd-bitwidth FCS", {
filename <- "Sample 2.fcs"
expect_error(fr <- load_cytoframe_from_fcs(file.path(dataPath, filename)), "Sorry, C parser doesn't support odd bitwidth!")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
# keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["Sample2"]], digest(fr))
filename <- "11ColorSmall.fcs"
expect_error(fr <- load_cytoframe_from_fcs(file.path(dataPath, "oddbitwith", filename)), "Sorry, C parser doesn't support odd bitwidth!")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
# keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["11ColorSmall"]], summary(fr))
#too slow to test
# fr <- read.FCS(file.path(dataPath, "oddbitwith/11ColorForOthers.fcs"))
# keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["11ColorForOthers"]], digest(fr))
# fr <- read.FCS("file.path(dataPath, "oddbitwith/11ColorFull.fcs"))
# keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["11ColorFull"]], digest(fr))
})
# CHANGE: Due to the differing structure of cytoframe vs flowFrame, we shouldn't expect these to hash the same.
# So for now just disable all digest() checks and add simple "expect_is(obj ,cytoframe)" checks for completion.
test_that("test other FCS", {
filename <- "20110125240_F06_I025.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["ITN029ST"]], digest(fr))
fr <- load_cytoframe_from_fcs(list.files(system.file("extdata", package="flowCore"),full=T)[1])
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["flowCore"]], digest(fr))
filename <- "Blank.FCS"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
expect_equal(expectRes[["read.FCS"]][["Blank"]], summary(fr))
filename <- "Bendall et al Cell Sample A_basal.fcs"
expect_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
, "dropped")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["Bendall"]], digest(fr))
})
test_that("test delimiter issue", {
filename <- "GFP_2Kfold_011911_noKan_QA-1.fcs"
expect_error(load_cytoframe_from_fcs(file.path(dataPath, filename))
, "Empty keyword name detected")
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename), emptyValue = F)
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
expect_equal(expectRes[["read.FCS"]][["GFP2Kfold"]], summary(fr))
expect_match(keyword(fr)[["GTI$WORKLIST"]], "C:/Document")
filename <- "RAINBOW_OK.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["RAINBOW"]], digest(fr))
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename), emptyValue = F)
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["RAINBOWEmptyValue"]], digest(fr))
#\ as delimiter with empty value
filename <- "sample_1071.001"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["sample1071"]], digest(fr))
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename),emptyValue=F)
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["sample1071.double"]], digest(fr))
})
# latest R no longer permit overflowed coersion by as.integer
test_that("test Beckman_Coulter_XDP issue", {
frList <- lapply(list.files(file.path(dataPath, "Beckman_Coulter/Beckman_Coulter_XDP/"),full=T)
, function(thisFile){
fr <- load_cytoframe_from_fcs(thisFile)
keyword(fr)[["FILENAME"]] <- "setToDummy"
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
# expect_equal(expectRes[["read.FCS"]][["BeckmanCoulterXDP"]], digest(frList))
})
test_that("test Beckman_Coulter $SPILLOVER keyword", {
frList <- lapply(list.files(file.path(dataPath, "Beckman_Coulter"),full=T, pattern = ".fcs")
, function(thisFile){
fr <- load_cytoframe_from_fcs(thisFile)
keyword(fr)[["FILENAME"]] <- "setToDummy"
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
# expect_equal(expectRes[["read.FCS"]][["BeckmanCoulterSPILLOVER"]], digest(frList))
})
test_that("test U mode", {
expect_error(load_cytoframe_from_fcs(file.path(dataPath, "PartecPAI/A0006980.FCS"))
, "MODE U")
})
test_that("test pre-gated data", {
filename <- "HC002_Col1_P3.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["HC002_Col1_P3"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
filename <- "HC002_Col1.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["HC002_Col1"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
test_that("test flowJo exported data with offset = 99999999 and missing the $BEGINDATA and $ENDDATA keywords ", {
filename <- "badFlowJoExport.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["badFlowJoExport"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
test_that("test integer overflow issue", {
filename <- "intOverFlow.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["intOverFlow"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
filename <- "MoFlo Astrios EQ 9C bis all.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath,"/Beckman_Coulter", filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["MoFlo EQ 9C"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
test_that("test diverse Bitwidths", {
filename <- "diverseBitwidths.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["diverseBitwidths"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
test_that("handle > 2^32-1 bytes", {
fr <- flowFrame(matrix(data = rnorm(3e8), nrow = 1e8, ncol =3, dimnames = list(NULL, c("A", "B", "C"))))
expect_gt(object.size(exprs(fr)), 2^31-1)
tmp <- tempfile()
write.FCS(fr, tmp, what = "double")
set.seed(1)
lines <- sort(sample(1:1e8, 1e3))
fr1 <- load_cytoframe_from_fcs(tmp, which.lines = lines)
expect_equivalent(exprs(fr)[lines,], exprs(fr1))
})
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context("Functional Tests Related to Loading/Saving cytoframes from FCS")
# adapted from flowCore IO-testSuite.R
library(digest)
dataPath <- "~/rglab/workspace/flowCore/misc/"
expectRes <- readRDS("~/rglab/workspace/flowCore/tests/testthat/expectResults.rds")
expectRes.new <- readRDS("~/rglab/workspace/flowCore/tests/testthat/expectRes.new.rds")
# NOTE: These tests are adapted for load_cytoframe_from_fcs() with as few changes as possible from the I/O tests for
# read.FCS() from flowCore's IO-testSuite.R. Where a test was changed due to expected changes in behavior
# between cytoframe and flowFrame or between load_cytoframe_from_fcs() and read.FCS(), those were indicated
# with "CHANGE". Many tests will require further adaptation (particularly those relying on digest()), so
# this is a work in progress. All comments (and commented-out lines) were left intact.
# saveRDS(expectRes.new, file = "~/rglab/workspace/flowCore/tests/testthat/expectRes.new.rds")
# test_that("Miltenyi's Macsquantify", {
# expect_warning(
# fr <- read.FCS(file.path(dataPath, "Miltenyi/1696_12017-04-30.0001_compatible.fcs"))
# , "Missing the required")
# expect_is(fr, "flowFrame")
#
# range(fr, type = "data")
# range(fr)
# expect_warning(fr <- read.FCS(file.path(dataPath, "double_precision/wishbone_thymus_panel1_rep1.fcs")), "Missing the required")
#
# expect_equal(nrow(fr), 250170)
#
# })
# expectRes.new <- list()
test_that("big file", {
#too slow to run
# fr <- read.FCS(file.path(dataPath, "gigantic_file.fcs"), column.pattern = "FSC*")
# CHANGE -- cytoset errors out for this, while trunk does not
fr <- expect_error(load_cytoframe_from_fcs(file.path(dataPath, "gigantic_file.fcs")
, which.lines = c(1,1e9)
, column.pattern = "FSC*"), "which.lines exceeds the data boundary")
# expect_equal(nrow(fr), 1)
fr <- load_cytoframe_from_fcs(file.path(dataPath, "gigantic_file.fcs"), which.lines = 1:1e3)
expect_equal(nrow(fr), 1e3)
fr <- load_cytoframe_from_fcs(file.path(dataPath, "gigantic_file.fcs"), which.lines = (1e3+1):2e3)
expect_equal(nrow(fr), 1e3)
})
# CHANGE: warnings are just console output for now. So all "expect_warning" calls are now "expect_output".
test_that("DATATYPE:'D'", {
expect_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, "double_precision/wishbone_myleoid_monocyte.fcs")), "warning:Missing the required")
expect_is(fr, "cytoframe")
filename <- "wishbone_thymus_panel1_rep1.fcs"
msg <- capture_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, "double_precision", filename)))
expect_match(msg, "Missing the required")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
expect_equal(nrow(fr), 250170)
})
test_that("multi data segment", {
expect_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, "multi-datasegment.fcs")), "additional data segment")
expect_is(fr, "cytoframe")
expect_equal(nrow(fr), 1244)
filename <- "multi-datasegment.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename), dataset = 1)
expect_equal(nrow(fr), 1244)
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename), dataset = 10)
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
expect_equal(nrow(fr), 955)
})
test_that("FCS with both SPILL and $SPILLOVER present", {
filename <- "example-spill-spillover.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
expect_equal(keyword(fr)[["SPILL"]], keyword(fr)[["$SPILLOVER"]])
# CHANGE: spillover() now will allow direct specfication of keyword, but only returns single matrix
tmp1 <- spillover(fr)
tmp2 <- spillover(fr, "$SPILLOVER")
expect_equal(tmp1, tmp2)
tmp <- tempfile()
write.FCS(fr, filename = tmp)
fr <- load_cytoframe_from_fcs(tmp)
expect_equal(keyword(fr)[["SPILL"]], keyword(fr)[["$SPILLOVER"]])
})
test_that("test uint_64 + diverse bitwidths + missing $NEXTDATA: '*' ", {
filename <- "uint_64.lxb"
# CHANGE: This warning is not implemented in load_cytoframe_from_fcs as it is in read.FCS.
# If '$PnE' not found, just defaults to '0,0' silently. Leaving the check in for now, but failure is expected.
expect_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, filename)), "No '$PnE' keyword")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
})
#TODO: investigate why the results is no longer consistent with the archived summary
test_that("mixed endian", {
filename <- "mixedEndian.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
expect_is(fr, "cytoframe")
# expect_equal(summary(fr), expectRes[["read.FCS"]][["mixedEndian"]])
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
})
# 'FILENAME' keyword may change when file path is changed
# so we hard code it to make the comparsion consistent in case the file is moved
test_that("test special delimiter character: '*' ", {
filename <- "multi_data_segment.LMD"
expect_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, filename)), "additional data segment")
expect_equal(summary(fr), expectRes[["read.FCS"]][["multi_data_segment"]], tolerance = 0.08)
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
})
test_that("test special delimiter character: '*' ", {
filename <- "specialDelimiter.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
expect_equal(summary(fr), expectRes[["read.FCS"]][["specialDelimiter"]], tolerance = 0.001)
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
})
test_that("test flowJo exported data with missing some of PnR keywords ", {
expect_output(expect_error(fr <- load_cytoframe_from_fcs(file.path(dataPath, "missing_PnR_flowJoExport.fcs"))
, "not contained"), "warning:Missing the required \\$BEGINDATA keyword")
})
test_that("test in consistent datastart between header and TEXT", {
expect_output(expect_error(fr <- load_cytoframe_from_fcs(file.path(dataPath, "Accuri-C6", "Accuri - C6 - A02 Spherotech 8 Peak Beads.fcs"), emptyValue = FALSE)
, "HEADER and the TEXT")
, "uneven number of tokens")
filename <- "Accuri - C6 - A02 Spherotech 8 Peak Beads.fcs"
msg <- capture_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, "Accuri-C6", filename), emptyValue = FALSE, ignore.text.offset = TRUE))
expect_match(msg, "HEADER and the TEXT")
expect_match(msg, "uneven number of tokens")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
expect_equal(nrow(fr), 60661)
expect_equal(summary(fr), expectRes[["read.FCS"]][["Accuri-C6"]], tolerance = 0.001)
msg <- capture_output(fs <- load_cytoset_from_fcs(file.path(dataPath, "Accuri-C6", filename), emptyValue = FALSE, ignore.text.offset = TRUE))
expect_match(msg, "HEADER and the TEXT")
expect_match(msg, "uneven number of tokens")
expect_equal(nrow(fs[[1]]), 60661)
})
# CHANGE: C parser errors on odd bitwidth, so disable tests subsequent to parse attempt.
test_that("test odd-bitwidth FCS", {
filename <- "Sample 2.fcs"
expect_error(fr <- load_cytoframe_from_fcs(file.path(dataPath, filename)), "Sorry, C parser doesn't support odd bitwidth!")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
# keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["Sample2"]], digest(fr))
filename <- "11ColorSmall.fcs"
expect_error(fr <- load_cytoframe_from_fcs(file.path(dataPath, "oddbitwith", filename)), "Sorry, C parser doesn't support odd bitwidth!")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
# keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["11ColorSmall"]], summary(fr))
#too slow to test
# fr <- read.FCS(file.path(dataPath, "oddbitwith/11ColorForOthers.fcs"))
# keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["11ColorForOthers"]], digest(fr))
# fr <- read.FCS("file.path(dataPath, "oddbitwith/11ColorFull.fcs"))
# keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["11ColorFull"]], digest(fr))
})
# CHANGE: Due to the differing structure of cytoframe vs flowFrame, we shouldn't expect these to hash the same.
# So for now just disable all digest() checks and add simple "expect_is(obj ,cytoframe)" checks for completion.
test_that("test other FCS", {
filename <- "20110125240_F06_I025.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["ITN029ST"]], digest(fr))
fr <- load_cytoframe_from_fcs(list.files(system.file("extdata", package="flowCore"),full=T)[1])
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["flowCore"]], digest(fr))
filename <- "Blank.FCS"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
expect_equal(expectRes[["read.FCS"]][["Blank"]], summary(fr))
filename <- "Bendall et al Cell Sample A_basal.fcs"
expect_output(fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
, "dropped")
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["Bendall"]], digest(fr))
})
test_that("test delimiter issue", {
filename <- "GFP_2Kfold_011911_noKan_QA-1.fcs"
expect_error(load_cytoframe_from_fcs(file.path(dataPath, filename))
, "Empty keyword name detected")
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename), emptyValue = F)
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
expect_equal(expectRes[["read.FCS"]][["GFP2Kfold"]], summary(fr))
expect_match(keyword(fr)[["GTI$WORKLIST"]], "C:/Document")
filename <- "RAINBOW_OK.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["RAINBOW"]], digest(fr))
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename), emptyValue = F)
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["RAINBOWEmptyValue"]], digest(fr))
#\ as delimiter with empty value
filename <- "sample_1071.001"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["sample1071"]], digest(fr))
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename),emptyValue=F)
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["sample1071.double"]], digest(fr))
})
# latest R no longer permit overflowed coersion by as.integer
test_that("test Beckman_Coulter_XDP issue", {
frList <- lapply(list.files(file.path(dataPath, "Beckman_Coulter/Beckman_Coulter_XDP/"),full=T)
, function(thisFile){
fr <- load_cytoframe_from_fcs(thisFile)
keyword(fr)[["FILENAME"]] <- "setToDummy"
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
# expect_equal(expectRes[["read.FCS"]][["BeckmanCoulterXDP"]], digest(frList))
})
test_that("test Beckman_Coulter $SPILLOVER keyword", {
frList <- lapply(list.files(file.path(dataPath, "Beckman_Coulter"),full=T, pattern = ".fcs")
, function(thisFile){
fr <- load_cytoframe_from_fcs(thisFile)
keyword(fr)[["FILENAME"]] <- "setToDummy"
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
# expect_equal(expectRes[["read.FCS"]][["BeckmanCoulterSPILLOVER"]], digest(frList))
})
test_that("test U mode", {
expect_error(load_cytoframe_from_fcs(file.path(dataPath, "PartecPAI/A0006980.FCS"))
, "MODE U")
})
test_that("test pre-gated data", {
filename <- "HC002_Col1_P3.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["HC002_Col1_P3"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
filename <- "HC002_Col1.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["HC002_Col1"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
test_that("test flowJo exported data with offset = 99999999 and missing the $BEGINDATA and $ENDDATA keywords ", {
filename <- "badFlowJoExport.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["badFlowJoExport"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
test_that("test integer overflow issue", {
filename <- "intOverFlow.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["intOverFlow"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
filename <- "MoFlo Astrios EQ 9C bis all.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath,"/Beckman_Coulter", filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["MoFlo EQ 9C"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
test_that("test diverse Bitwidths", {
filename <- "diverseBitwidths.fcs"
fr <- load_cytoframe_from_fcs(file.path(dataPath, filename))
#expectRes.new[[filename]] <<- list(ncol = ncol(fr), nrow = nrow(fr), chnl = colnames(fr), marker = markernames(fr), range = range(fr), range_data= range(fr, "data"), colmean = colMeans(exprs(fr)))
keyword(fr)[["FILENAME"]] <- "setToDummy"
# expect_equal(expectRes[["read.FCS"]][["diverseBitwidths"]], digest(fr))
expect_is(fr, "cytoframe") # Simple check of parse completion until better checks put in place
})
test_that("handle > 2^32-1 bytes", {
fr <- flowFrame(matrix(data = rnorm(3e8), nrow = 1e8, ncol =3, dimnames = list(NULL, c("A", "B", "C"))))
expect_gt(object.size(exprs(fr)), 2^31-1)
tmp <- tempfile()
write.FCS(fr, tmp, what = "double")
set.seed(1)
lines <- sort(sample(1:1e8, 1e3))
fr1 <- load_cytoframe_from_fcs(tmp, which.lines = lines)
expect_equivalent(exprs(fr)[lines,], exprs(fr1))
})
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