context("parse workspaces of various flowJo versions ")
library(data.table)
path <- "~/rglab/workspace/CytoML/wsTestSuite"
test_that("ellipsoidGate bug",{
# ellipse defined on fsc and ssc wasn't properly scaled
thisPath <- file.path(path, "Cytotrol/NHLBI/")
wsFile <- file.path(thisPath, "ellipse_bug.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, subset = 1)
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 2e-2)
})
test_that("verify the extend logic no longer needed for the gate defined in biexp scale from latest flowjo wsp output",{
wsFile <- file.path(path, "gate_negative_area.wsp")
ws <- open_flowjo_xml(wsFile)
thispath <- system.file("extdata", package = "flowWorkspaceData")
gs <- flowjo_to_gatingset(ws, name=1, path = thispath, extend_val = -Inf)
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 0.0003)
})
test_that("bypass faulty node",{
wsFile <- file.path(path, "bypassfaultynode.xml")
ws <- open_flowjo_xml(wsFile)
expect_error(gs <- flowjo_to_gatingset(ws, name = 4, path = file.path(path,"Cytotrol/NHLBI/Tcell/"), subset = 1), "colname not", class = "error")
gs <- flowjo_to_gatingset(ws, name = 4, path = file.path(path,"Cytotrol/NHLBI/Tcell/"), subset = 1, skip_faulty_gate = TRUE)
expect_equal(length(gs_get_pop_paths(gs)), 24)
expect_is(gh_pop_get_count(gs[[1]], "CD3+"), "numeric")
expect_true(is.na(gh_pop_get_count(gs[[1]], "CD4")))
})
test_that("Attribute redefined",{
skip("only run interactively due to its lengthy output that can't be suppressed")
wsFile <- file.path(path, "attr_redefined_err.xml")
expect_error(ws <- open_flowjo_xml(wsFile), "not parsed", class = "error")
suppressMessages(ws <- open_flowjo_xml(wsFile, options = 1))
expect_is(ws, "flowjo_workspace")
})
test_that("no gate",{
wsFile <- file.path(path, "no-gate.wsp")
ws <- open_flowjo_xml(wsFile, sample_names_from = 'sampleNode')
expect_equal(nrow(fj_ws_get_samples(ws)), 1)
gs <- flowjo_to_gatingset(ws, name = 1, path = file.path(path,"Cytotrol/NHLBI/Tcell/"), include_empty_tree = TRUE)
expect_equal(range(gh_pop_get_data(gs[[1]]))[,5], c(50.70029, 256.91464), tol = 1e-6)
expect_equal(length(gs_get_pop_paths(gs)), 1)
})
test_that("flog-- offset and decades that expose the previous logGml2-based flog was wrong",{
wsFile <- file.path(path, "flog/log.wsp")
ws <- open_flowjo_xml(wsFile, sample_names_from = 'sampleNode')
gs <- flowjo_to_gatingset(ws, name = 1, path = file.path(path,"Cytotrol/NHLBI/Tcell/"))
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 0.01)
})
test_that("which.lines",{
wsFile <- file.path(path, "flog_PnE/Liver.wsp")
ws <- open_flowjo_xml(wsFile, sample_names_from = 'sampleNode')
set.seed(1)
gs <- flowjo_to_gatingset(ws, name = 2, which.lines = 5e4)
expect_equal(nrow(gh_pop_get_data(gs[[1]])), 5e4)
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 0.04)
})
test_that("derived parameters",{
wsFile <- file.path(path, "derivedparam.wsp")
ws <- open_flowjo_xml(wsFile)
# flowWorkspace::set_log_level("GatingSet")
gs <- flowjo_to_gatingset(ws, name = 1, execute = F)
# set_log_level("none")
expect_equal(gs_get_pop_paths(gs, path = "auto")[-1], c("Lymphocytes", "CD3"))
})
test_that("set T value properly through PnE instead of PnR for flog transform when FCS data is log scale",{
wsFile <- file.path(path, "flog_PnE/Liver.wsp")
ws <- open_flowjo_xml(wsFile, sample_names_from = 'sampleNode')
gs <- flowjo_to_gatingset(ws, name = 2)
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 0.015)
})
test_that("handle the linear transform with maxRange = 0",{
wsFile <- file.path(path, "faultylinearTransform/FlowJo_Test.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1)
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq])
})
test_that("skip ManuallyIncludedSamples",{
wsFile <- file.path(path, "logicle.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, path = system.file("extdata", package = "flowCore"), fcs_file_extension = ".B08")
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 0.009)
})
test_that("skip ManuallyIncludedSamples",{
wsFile <- file.path(path, "ManuallyIncludedSamples.wsp")
ws <- open_flowjo_xml(wsFile)
expect_true(setequal(subset(fj_ws_get_sample_groups(ws), groupName == "Sample")[["sampleID"]], c(1:5, 21:25)))
gs <- flowjo_to_gatingset(ws, name = 3, path = file.path(path), execute = FALSE)
expect_is(gs, "GatingSet")
})
test_that("Handle duplicate sample names",{
wsFile <- file.path(path, "duplicatedSampleID", "Ustekin_G26_sas_IMMPORT2.495809.xml")
ws <- open_flowjo_xml(wsFile)
sink(tempfile())
expect_error(flowjo_to_gatingset(ws, name = 1), "Duplicated", class = "error")
gs <- suppressWarnings(flowjo_to_gatingset(ws, name = 1, additional.sampleID = TRUE, which.lines = 1))
sink()
expect_is(gs, "GatingSet")
})
test_that("search reference node for boolean gate ",{
thisPath <- file.path(path, "searchRefNode")
wsFile <- file.path(thisPath, "2583-Y-MAL067-FJ.xml")
ws <- open_flowjo_xml(wsFile)
gs <- suppressWarnings(flowjo_to_gatingset(ws, name="Samples", subset = "1379326.fcs"))
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(nrow(res), 235)
expect_equal(res[-10, xml.freq], res[-10, openCyto.freq], tol = 0.006)
expect_equal(res[10, openCyto.count], 164)
#skip leaf bool
gs <- suppressWarnings(flowjo_to_gatingset(ws, name="Samples", subset = "1379326.fcs", leaf.bool = F))
gh <- gs[[1]]
leaf.bool <- which(sapply(gs_get_pop_paths(gs), function(node)length(gs_pop_get_children(gh, node))==0&&gh_pop_is_bool_gate(gh,node)))
res <- gh_pop_compare_stats(gh)
expect_true(all(is.na(res[leaf.bool, openCyto.count])))
expect_equal(res[-leaf.bool, xml.freq], res[-leaf.bool, openCyto.freq], tol = 0.006)
})
test_that("vertical ellipsoidGate for vX ",{
thisPath <- file.path(path, "ellipsoid_vertical")
wsFile <- file.path(thisPath, "20171103.circle.flow.ctl.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- suppressWarnings(flowjo_to_gatingset(ws, name=1))
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 0.02)
})
test_that("skip gains from FCS for vX ",{
thisPath <- file.path(path, "no_gains_vX")
wsFile <- file.path(thisPath, "10-Apr-2017.wsp")
ws <- open_flowjo_xml(wsFile)
capture.output( gs <- flowjo_to_gatingset(ws, name=2))
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 1e-3)
})
#somehow the latest Rstudio crashes on this particular test case (but not in R console command)
test_that("gate extension ",{
thisPath <- file.path(path, "gate_extension")
wsFile <- file.path(thisPath, "02-15-2013_ICS.xml")
ws <- open_flowjo_xml(wsFile)
set.seed(1)
capture.output(gs <- flowjo_to_gatingset(ws, name=3, which.lines = 5e4))
res <- gh_pop_compare_stats(gs[[1]])[xml.count != -1, ]
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 3e-2)
})
test_that("curlyQuad gate1 ",{
thisPath <- file.path(path, "gate_extension")
wsFile <- file.path(thisPath, "VSVG_OGH_14OCT15.wsp")
ws <- open_flowjo_xml(wsFile)
capture.output(gs <- flowjo_to_gatingset(ws, name=3))
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 2e-3)
})
test_that("curlyQuad gate1 ",{
thisPath <- file.path(path, "curlyQuad/example1")
wsFile <- file.path(thisPath, "20151208_TBNK_DS.xml")
ws <- open_flowjo_xml(wsFile)
capture.output(gs <- flowjo_to_gatingset(ws, name=2))
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 7e-3)
})
test_that("curlyQuad gate ",{
thisPath <- file.path(path, "curlyQuad/example2")
wsFile <- file.path(thisPath, "20-Apr-2016.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name=1)
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 1.6e-2)
})
test_that("EllipsoidGate defined on log-transformed channels ",{
thisPath <- file.path(path, "ellipsoid_log")
wsFile <- file.path(thisPath, "xml_spillover2.xml")
ws <- open_flowjo_xml(wsFile, sample_names_from = "sampleNode")
capture.output(gs <- flowjo_to_gatingset(ws, name=1, execute = T, subset = "spillover_B2.fcs"))
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.count], res[, openCyto.count], tol = 4e-3)
})
test_that("No gate extension ",{
thisPath <- file.path(path, "negCoordinates")
wsFile <- file.path(thisPath, "08-Mar-2016.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, subset = 1) #default extend_val = 0 will extend the gate
res <- gh_pop_compare_stats(gs[[1]])
expect_gt(res[11, abs(xml.freq - openCyto.freq)], 0.1)
gs <- flowjo_to_gatingset(ws, name = 1, extend_val = -2e3)#relax the threshold to disable extension
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 4e-3)
})
test_that("FCS searching path with symlink ",{
thisPath <- file.path(path, "flin_symlink")
wsFile <- file.path(thisPath, "A01.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, subset = 1)
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 9e-4)
})
test_that("Time gate ",{
thisPath <- file.path(path, "flin")
wsFile <- file.path(thisPath, "A01.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, subset = 1)
res <- gh_pop_compare_stats(gs[[1]])
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 9e-4)
})
test_that("Time gate2--when computed timestep is very different from $TIMESTEP ",{
thisPath <- file.path(path, "timegate")
wsFile <- file.path(thisPath, "MX1_Analysis_VISC.xml")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws,name="Group 1",subset=1)
res <- gh_pop_compare_stats(gs[[1]])[xml.count!=-1,]
expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 8e-3)
})
test_that("Inverse function of flog ",{
thisPath <- file.path(path, "inverse")
wsFile <- file.path(thisPath, "Small.xml")
ws <- open_flowjo_xml(wsFile)
capture.output(gs <- flowjo_to_gatingset(ws, name=1, emptyValue=FALSE))
gh <- gs[[1]]
thisCounts <- gs_pop_get_count_fast(gs, path = "auto")
expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
expect_equal(thisCounts, expectCounts)
trans <- gh_get_transformations(gh)
inverse <- gh_get_transformations(gh, inverse = T)
raw <- c(1e2, 1e3,1e5)
log <- trans[[1]](raw)
expect_equal(inverse[[1]](log), raw)
})
test_that("v 10.0.6 - vX 1.8",{
thisPath <- file.path(path, "mssm")
wsFile <- file.path(thisPath, "CFSP_Analysis14.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = "Bcell", subset = 1, execute = FALSE)
expect_is(gs, "GatingSet")
gs <- flowjo_to_gatingset(ws, name = "Bcell", subset = 1)
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[-1, xml.count], thisCounts[-1, openCyto.count], tol = 3.7e-3)
#test double delimiter issue
fcsname <- pData(gs)[["name"]]
fr <- read.FCS(file.path(thisPath, fcsname))
tmp <- tempdir()
suppressWarnings(write.FCS(fr, filename = file.path(tmp, fcsname), delimiter = "/"))
expect_error(gs <- flowjo_to_gatingset(ws, name = "Bcell", subset = 1, path = tmp, emptyValue = T)
, "Empty keyword name", class = "error")#ncdfFlowSet
gs <- flowjo_to_gatingset(ws, name = "Bcell", subset = 1, path = tmp, emptyValue = F)#ncdf
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[-1, xml.count], thisCounts[-1, openCyto.count], tol = 3.7e-3)
# gs <- flowjo_to_gatingset(ws, name = "Bcell", subset = 1, isNcdf = F, path = tmp, emptyValue = F)#flowSet
# gh <- gs[[1]]
# thisCounts <- gh_pop_compare_stats(gh)
# expect_equal(thisCounts[-1, xml.count], thisCounts[-1, openCyto.count], tol = 3.7e-3)
})
test_that("v 10.0.7 - vX 20.0 (ellipsoidGate)",{
thisPath <- file.path(path, "bioaster_ellipsoidGate")
wsFile <- file.path(thisPath, "Matrice_1.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = "Matrice", subset = 1, execute = FALSE)
expect_is(gs, "GatingSet")
gs <- flowjo_to_gatingset(ws, name = "Matrice", subset = 1)
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 2e-2)
})
test_that("v 10.0.7 - vX 20.0 (missing_namespace and flin)",{
thisPath <- file.path(path, "missing_namespace")
wsFile <- file.path(thisPath, "BM_data.xml")
ws <- open_flowjo_xml(wsFile, options = 32)#set option to suppress xml error
expect_error(gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, execute = FALSE)
, "*: unknown tranformation type!transforms:linear", class = "error")
wsFile <- file.path(thisPath, "BM_data_corrected.xml")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, execute = FALSE)
expect_is(gs, "GatingSet")
gh <- gs[[1]]
trans <- gh_get_transformations(gh, only = F, channel = "all")
expect_equal(trans[[2]][["name"]], "flowJo_log")
})
# invalid xml with Namespace prefix defintion missing #TODO: try to be robust on this kind of xml error
#test_that("v 10.0.7 - vX 20.0 (McGill/BMDCs) linear transformation",{
#
# thisPath <- file.path(path, "McGill/BMDCs")
# wsFile <- file.path(thisPath, "20140124 BMDCs.1.wsp")
#
# ws <- open_flowjo_xml(wsFile)
# gs <- flowjo_to_gatingset(ws, name = 3, subset = 1, execute = FALSE)
# expect_is(gs, "GatingSet")
# gs <- flowjo_to_gatingset(ws, name = 3, subset = 1)
#
# gh <- gs[[1]]
# expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
# thisCounts <- gh_pop_compare_stats(gh)[, list(xml.count,openCyto.count, node)]
# expect_equal(thisCounts, expectCounts)
# })
test_that("v 10.0.7 - vX 20.0 (McGill/treg) ellipseidGate (biexponential)",{
thisPath <- file.path(path, "McGill/Treg")
wsFile <- file.path(thisPath, "20131206_Treg.1.ellipseidGate.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 3, subset = 4, execute = FALSE)
expect_is(gs, "GatingSet")
g <- gh_pop_get_gate(gs[[1]], "CD4Ellipse")
#transformed ellipse Gate
expect_is(g, "polygonGate")
expect_equal(range(g@boundaries[, "Comp-APC-A"]), c(143.918, 207.082), tol = 1e-6)
expect_equal(range(g@boundaries[, "SSC-A"]), c(10168.56, 58439.45), tol = 1e-6)
#skip gate transform
gs <- flowjo_to_gatingset(ws, name = 3, subset = 4, execute = FALSE, transform = FALSE)
g <- gh_pop_get_gate(gs[[1]], "CD4Ellipse")
expect_is(g, "polygonGate")
#ellipsoidGate should be in 256 * 256 scale
expect_equal(range(g@boundaries[, "Comp-APC-A"]), c(143.918, 207.082), tol = 1e-6)
expect_equal(range(g@boundaries[, "SSC-A"]), c(9.930231, 57.069771), tol = 1e-6)
gs <- flowjo_to_gatingset(ws, name = 3, subset = 4)
gh <- gs[[1]]
# expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[,xml.freq], thisCounts[,openCyto.freq], tol = 7e-4)
})
test_that("v 10.0.7 - vX 20.0 (PROVIDE/CyTOF) ellipseidGate (fasinh)",{
thisPath <- file.path(path, "PROVIDE")
wsFile <- file.path(thisPath, "batch1_local_and_week_53.wsp")
ws <- open_flowjo_xml(wsFile, sample_names_from = "sampleNode")
gs <- flowjo_to_gatingset(ws, name = 1, subset = 3, execute = FALSE)
expect_is(gs, "GatingSet")
#won't find the file if $TOT is taken into account(most likely the data provided was wrong)
expect_output(expect_error(gs <- flowjo_to_gatingset(ws, name = 1, subset = 3)
, "No samples", class = "error")
, "FCS")
#relax the rules
# UPDATE: After changes to search_for_fcs, this kind of evasion of $TOT check is not possible
expect_error(capture.output(gs <- flowjo_to_gatingset(ws, name = 1, subset = 3, additional.keys = NULL)), "No samples", class = "error")
#switch to the corrected wsp
wsFile <- file.path(thisPath, "count_corrected.wsp")
ws <- open_flowjo_xml(wsFile, sample_names_from = "sampleNode")
capture.output(gs <- flowjo_to_gatingset(ws, name = 1, subset = 3))
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)[, list(xml.count,openCyto.count, node)]
expect_equal(thisCounts[, openCyto.count], thisCounts[, xml.count], tol = 0.04)
})
test_that("v 10.0.7 - vX 20.0 (cytof no compensation)",{
thisPath <- file.path(path, "CyTOF")
wsFile <- file.path(thisPath, "cytof.wsp")
ws <- open_flowjo_xml(wsFile)
expect_warning(gs <- flowjo_to_gatingset(ws, name = 1, path = file.path(path), execute = FALSE), "different gating tree structures")
expect_is(gs, "GatingSet")
# gh <- gs[[1]]
# expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
# thisCounts <- gh_pop_compare_stats(gh)[, list(xml.count,openCyto.count, node)]
# expect_equal(thisCounts, expectCounts)
})
test_that("v 10.0.7r2 - vX 20.0 (NotNode)",{
thisPath <- file.path(path, "combineNode/NotNode")
wsFile <- file.path(thisPath, "WSwithNotNodePopulation.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, path = file.path(path), execute = FALSE)
expect_is(gs, "GatingSet")
gh <- gs[[1]]
g <- gh_pop_get_gate(gh, "CD20+⁻")
expect_is(g, "booleanFilter")
expect_equal(g@deparse, "!LIVE/Single Cells/CD45+/CD20+")
expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
thisCounts <- gh_pop_compare_stats(gh)[, list(xml.count,openCyto.count, node)]
expect_equivalent(thisCounts[,c("xml.count", "node"), with = F], expectCounts[,c("flowJo.count", "node"), with = F])
})
test_that("v 10.2 - vX 20.0 (AndNode)",{
thisPath <- file.path(path, "combineNode/AndNode")
wsFile <- file.path(thisPath, "test_gates.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, path = file.path(path), execute = FALSE)
expect_is(gs, "GatingSet")
gh <- gs[[1]]
g <- gh_pop_get_gate(gh, "CD4/CD107+IFNg+IL2+Mip1b+TNF+")
expect_is(g, "booleanFilter")
expect_equal(g@deparse, "Lymphocytes/Single Cells/CD3/CD4/CD107&Lymphocytes/Single Cells/CD3/CD4/IFNg&Lymphocytes/Single Cells/CD3/CD4/IL2&Lymphocytes/Single Cells/CD3/CD4/Mip1b&Lymphocytes/Single Cells/CD3/CD4/TNF")
})
test_that("v 10.0.8r1 - vX 20.0 (OrNode)",{
thisPath <- file.path(path, "combineNode/OrNode")
wsFile <- file.path(thisPath, "Test_EW.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, path = thisPath)
expect_is(gs, "GatingSet")
gh <- gs[[1]]
g <- gh_pop_get_gate(gh, "CD44+")
expect_is(g, "booleanFilter")
expect_equal(g@deparse, "FCS singlets/SSC singlets/Lymphocytes/CD8/F5/Live/Q6: CD44+ , CD62L+|FCS singlets/SSC singlets/Lymphocytes/CD8/F5/Live/Q7: CD44+ , CD62L-")
expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
thisCounts <- gh_pop_compare_stats(gh)[, list(xml.count,openCyto.count, node)]
expect_equivalent(thisCounts, expectCounts)
})
test_that("v 10.0.8 - vX 20.0 (slash_issue_vX)",{
thisPath <- file.path(path, "slash_issue_vX")
wsFile <- file.path(thisPath, "IFEP004.wsp")
ws <- open_flowjo_xml(wsFile)
set.seed(1)
gs <- flowjo_to_gatingset(ws, name = 5, path = file.path(thisPath), which.lines = 1e5)
expect_is(gs, "GatingSet")
gh <- gs[[1]]
# expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 0.025)
})
test_that("v 10.2 - vX 20.0 (EllipsoidGate)",{
thisPath <- file.path(path, "EllipsoidGate_10.2")
wsFile <- file.path(thisPath, "mA_J21_for_HT.wsp")
ws <- open_flowjo_xml(wsFile)
set.seed(1)
gs <- flowjo_to_gatingset(ws, name = 2, path = file.path(thisPath), which.lines = 1e5)
expect_is(gs, "GatingSet")
gh <- gs[[1]]
# expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 0.03)
})
test_that("v 7.6.1- win 1.6 (use default biexp trans when channel-specific trans not found within its respective trans group )",{
thisPath <- file.path(path, "GYO")
wsFile <- file.path(thisPath, "whole_blood_GYO-0109_050214.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 2, subset = 1, path = thisPath, execute = FALSE)
expect_is(gs, "GatingSet")
set.seed(1)
expect_output(gs <- flowjo_to_gatingset(ws, name = 2, path = thisPath, which.lines = 1e5), "FCS")
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 0.015)
})
test_that("v 7.6.5 - win 1.61 (PBMC)",{
thisPath <- file.path(path, "PBMC/Blomberg")
wsFile <- file.path(thisPath, "Exp2_Tcell.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, sample_names_from = "sampleNode", execute = FALSE)
expect_is(gs, "GatingSet")
gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, sample_names_from = "sampleNode")
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 9e-3)
})
test_that("v 7.6.5 - win 1.61 (sample_names_from = 'sampleNode')",{
thisPath <- file.path(path, "Cytotrol/Miami")
wsFile <- file.path(thisPath, "flowJo/Cytotrol_061112_Tcell.wsp")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, path = file.path(thisPath,"Tcell"), sample_names_from = "sampleNode", execute = FALSE)
expect_is(gs, "GatingSet")
gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, path = file.path(thisPath,"Tcell"), sample_names_from = "sampleNode")
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 2e-4)
})
#this test case failed on the libxml parsing
# test_that("v 9.0.1 - mac 2.0 (HVTN RV144 -- options = 1)",{
#
# thisPath <- file.path(path, "HVTN/RV144")
# wsFile <- file.path(thisPath, "Batch 1264 RV144.xml")
#
# dd <- capture_output(ws <- open_flowjo_xml(wsFile, options = 1))
# #not sure how to suppress the long stacks of C messages (XML package)
# gs <- flowjo_to_gatingset(ws, name = 4, subset = 1, execute = FALSE)
# expect_is(gs, "GatingSet")
#
# gs <- flowjo_to_gatingset(ws, name = 4, subset = 1)
# gh <- gs[[1]]
# expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
# thisCounts <- gh_pop_compare_stats(gh)[, list(xml.count,openCyto.count, node)]
# expect_equal(thisCounts, expectCounts, tolerance = 1e-5, check.attributes = FALSE)
#
# })
#
test_that("v 9.0.1 - mac 2.0 (HVTN 080-0880)",{
thisPath <- file.path(path, "HVTN/080")
wsFile <- file.path(thisPath, "080_batch_0880.xml")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 4, subset = 1, execute = FALSE)
expect_is(gs, "GatingSet")
set.seed(1)
gs <- flowjo_to_gatingset(ws, name = 4, subset = "431321.fcs", which.lines = 1e5)
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 4e-3)
})
test_that("v 9.2 - mac 2.0 (ITN029)",{
thisPath <- file.path(path, "ITN029ST")
wsFile <- file.path(thisPath, "QA_template.xml")
ws <- open_flowjo_xml(wsFile)
expect_output(gs <- flowjo_to_gatingset(ws, name = 2, subset = 1,execute = FALSE), "no calibration")
expect_is(gs, "GatingSet")
expect_output(gs <- flowjo_to_gatingset(ws, name = 2, subset = 1), "no calibration")
gh <- gs[[1]]
# expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
# thisCounts <- gh_pop_compare_stats(gh)[, list(xml.count,openCyto.count, node)]
# expect_equal(thisCounts, expectCounts, check.attributes = FALSE)
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 7e-3)
})
test_that("v 9.4.2 - mac 2.0",{
thisPath <- file.path(path, "PBMC/HIPC_trial")
wsFile <- file.path(thisPath, "data/HIPC_trial.xml")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 2, subset = 1, execute = FALSE)
expect_is(gs, "GatingSet")
gs <- flowjo_to_gatingset(ws, name = 2, subset = 1)
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 5e-3)
})
#1. boolean specification contains double spaces and non-spaces, which leads to the fix that uses boolean operator as delimiter instead of space)
#2. boolean gate refers to the node (AM) that appears both at sibling and children level, which leads to further checking in getRefNodes routines
#3. boolean gate has quotedString which leads to more generic xpath searching for gatePath and trailing space removal.
test_that("v 9.4.4 - mac 2.0 ",{
thisPath <- file.path(path, "JJ")
wsFile <- file.path(thisPath, "JJ_FlowJo_.xml")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = "Test", subset = 1, execute = FALSE)
expect_is(gs, "GatingSet")
set.seed(1)
gs <- flowjo_to_gatingset(ws, name = "Test", subset = 1, which.lines = 1e5)
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 2e-2)
})
test_that("v 9.5.2 - mac 2.0",{
thisPath <- file.path(path, "Cytotrol/NHLBI")
wsFile <- file.path(thisPath, "flowJo/NHLBI.xml")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 2, subset = 1, path = file.path(thisPath,"Bcell"), execute = FALSE)
expect_is(gs, "GatingSet")
gs <- flowjo_to_gatingset(ws, name = 2, subset = 1, path = file.path(thisPath,"Bcell"))
gh <- gs[[1]]
expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 5e-3)
#create a temp folder and symlink to original files to test the feature of searching sample by keyword $FIL
# in the use case where the fcs has been modified
fcs <- list.files(pattern = "fcs", file.path(thisPath, "Bcell"), full = T)[[1]]
tmp <- tempfile()
dir.create(tmp)
newFCS <- file.path(tmp, "test.fcs")
file.symlink(fcs, newFCS)
gs <- flowjo_to_gatingset(ws, name = 2, subset = 1, path = tmp)
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 5e-3)
unlink(tmp,recursive = T)
})
test_that("v 9.6.3 - mac 2.0 (ignore highValue for FSC/SSC)",{
thisPath <- file.path(path, "roch")
wsFile <- file.path(thisPath, "PROP_20120118_TPHE.xml")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 1, subset = "Specimen_001_Tube_024.fcs", execute = FALSE)
expect_is(gs, "GatingSet")
set.seed(1)
gs <- flowjo_to_gatingset(ws, name = 1, subset = "Specimen_001_Tube_024.fcs")
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 7e-3)
})
test_that("v 9.7.4 - mac 3.0",{
thisPath <- file.path(path, "v9.7.4")
wsFile <- file.path(thisPath, "T1_CHI-002v974.xml")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = "CHI-002_PBMC_control", subset = "CHI-002_PBMC_control_101211.fcs", execute = FALSE)
expect_is(gs, "GatingSet")
set.seed(1)
gs <- flowjo_to_gatingset(ws, name = "CHI-002_PBMC_control", subset = "CHI-002_PBMC_control_101211.fcs")
gh <- gs[[1]]
expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
thisCounts <- gh_pop_compare_stats(gh, path = "full")[, list(xml.count,openCyto.count, node)]
expectCounts[flowJo.count ==0, flowJo.count := -1]#fix the legacy counts
expect_equal(thisCounts, expectCounts, check.attributes = FALSE, tol = 3.3e-3)
})
test_that("v 9.7.5 - mac 3.0 (no compensation and using calibrationIndex)",{
thisPath <- file.path(path, "Ragon")
wsFile <- file.path(thisPath, "neut_v_non_neut_v9.xml")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 5, subset = "477889_env_cct_norm_concatenated.txt", execute = FALSE)
expect_is(gs, "GatingSet")
gs <- flowjo_to_gatingset(ws, name = 5, subset = "477889_env_cct_norm_concatenated.txt", fcs_file_extension = ".txt")
gh <- gs[[1]]
expectCounts <- fread(file.path(thisPath, "expectCounts.csv"))
thisCounts <- gh_pop_compare_stats(gh)[, list(xml.count,openCyto.count, node)]
expectCounts[flowJo.count ==0, flowJo.count := -1] #fix the legacy counts
expect_equal(thisCounts, expectCounts, check.attributes = FALSE, tol = 2e-4)
})
test_that("v 9.7.5 - mac 3.0 (boolGate that refers to the non-sibling nodes)",{
thisPath <- file.path(path, "094")
wsFile <- file.path(thisPath, "1851-M-094.xml")
ws <- open_flowjo_xml(wsFile)
gs <- flowjo_to_gatingset(ws, name = 2, subset = "434713.fcs", execute = FALSE)
expect_is(gs, "GatingSet")
set.seed(1)
gs <- flowjo_to_gatingset(ws, name = 2, subset = "434713.fcs", which.lines = 1e5)
gh <- gs[[1]]
thisCounts <- gh_pop_compare_stats(gh)
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 5e-3)
})
test_that("search_for_fcs logic", {
thisPath <- file.path(path, "file_search_tests")
wsFile <- file.path(thisPath, "manual.xml")
subset <- c("CytoTrol_CytoTrol_1.fcs", "CytoTrol_CytoTrol_2.fcs")
ws <- open_flowjo_xml(wsFile)
# Simple case, no subdirs and filenames match sampleNames
fcs_path <- file.path(thisPath, "no_subdirs")
gs <- flowjo_to_gatingset(ws, name=4, subset=subset, path=fcs_path)
expect_equal(length(gs), 2)
# This one should reject CytoTrol_CytoTrol_1.fcs because $TOT doesn't match
fcs_path <- file.path(thisPath, "no_subdirs_wrong_TOT")
msgs <- capture.output(gs <- flowjo_to_gatingset(ws, name=4, subset=subset, path=fcs_path))
expect_match(msgs[[1]], "incorrect total number of events",)
expect_equal(length(gs), 1)
# One of the filenames doesn't match, go to $FIL
fcs_path <- file.path(thisPath, "needs_FIL")
gs <- flowjo_to_gatingset(ws, name=4, subset=subset, path=fcs_path)
expect_equal(length(gs), 2)
# Toplevel directory file has wrong $TOT, so it should grab the one
# from the subdirectory
fcs_path <- file.path(thisPath, "needs_TOT")
gs <- flowjo_to_gatingset(ws, name=4, subset=subset, path=fcs_path)
expect_equal(length(gs), 2)
expect_match(keyword(gs[[1]], "FILENAME"), "subdir_with_correct_TOT/CytoTrol_CytoTrol_1.fcs")
# In toplevel $TUBE NAME on CytoTrol_CytoTrol_1.fcs changed CytoTrol_2 -> Cytotrol_2
# If no subdirs, accept lone match (no need to check keys)
fcs_path <- file.path(thisPath, "needs_keys", "no_subdirs")
gs <- flowjo_to_gatingset(ws, name=4, subset=subset, path=fcs_path)
expect_equal(length(gs), 2)
expect_match(keyword(gs[[2]], "FILENAME"), "no_subdirs/CytoTrol_CytoTrol_2.fcs")
# Now, with multiple $TOT matches, need to check keys and take the one from the subdir
fcs_path <- file.path(thisPath, "needs_keys", "w_subdirs")
# It should fail without specifying additional keys
expect_error(gs <- flowjo_to_gatingset(ws, name=4, subset=subset, path=fcs_path), "Multiple FCS files", class = "error")
gs <- flowjo_to_gatingset(ws, name=4, subset=subset, path=fcs_path, additional.keys = c("TUBE NAME"))
expect_equal(length(gs), 2)
expect_match(keyword(gs[[2]], "FILENAME"), "subdir_with_correct_keys/CytoTrol_CytoTrol_2.fcs")
# Just make sure it appropriately errors out for full duplicates
fcs_path <- file.path(thisPath, "full_duplicates")
expect_error(gs <- flowjo_to_gatingset(ws, name=4, subset=subset, path=fcs_path, additional.keys = c("TUBE NAME")), "Multiple FCS files", class = "error")
})
test_that("magnetic gates", {
thisPath <- file.path(path, "magnetic")
ws <- open_flowjo_xml(file.path(thisPath, "2020-03-11_CyTOF_gating_strategy_dummy.wsp"))
gs <- flowjo_to_gatingset(ws, name = 1)
thisCounts <- gh_pop_compare_stats(gs[[1]])
# Give a little cushion to frequency tolerance due to small subsample
expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 2e-2)
})
test_that("keep uncompensated channels", {
wsfile <- file.path(path, "comp_uncomp.wsp")
datapath <- system.file("extdata",package="flowWorkspaceData")
cf <- load_cytoframe_from_fcs(list.files(datapath, "CytoTrol_CytoTrol_1.fcs", full.names = TRUE))
ws <- open_flowjo_xml(wsfile);
gs1 <- flowjo_to_gatingset(ws, name = 1, path = datapath);
expect_equal(colnames(gs1),
c("FSC-A","FSC-H","FSC-W","SSC-A","Comp-B710-A","Comp-R660-A","Comp-R780-A","Comp-V450-A","Comp-V545-A","Comp-G560-A","Comp-G780-A","Time","B710-A"))
expected_dims <- dim(cf)
expected_dims["parameters"] <- expected_dims["parameters"] + 1
expect_equal(expected_dims, dim(gh_pop_get_data(gs1[[1]])))
})
