Dear all,
I was not successful in installing the flowIncubator package on Windows, however it was installed on my Mac through install_github("RGLab/flowIncubator").
I tried the function of flowIncubator tmix2DGate
on my data and it seems that the flowClustFast
function of openCyto that the flowIncubator is referring to is non-existent? When I compare my flowIncubator package files in the library on Windows vs Mac, they have a bit different number of files. Especially, there are no tmix2DGate.R in flowIncubator's R file. So, I tried to change the constituents of my flowIncubator on Mac, adding all missing files and still R does give this error:
my code: add_pop(gs, alias = "cd41,cd42,cd43", pop = "*", parent = "root", dims = "CD25,CD127", gating_method = "tmix2DGate.wrapper", gating_args = "K = 3, quantile = 0.6, trans = 0")
Error in (function (fs, pp_res, gFunc, popAlias, channels, gFunc_args) :
failed at Alcina TregMAIT_AV 10-1974 P1.fcs
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object '.flowClustFast' not found
when I do traceback()
traceback()
15: stop("failed at ", paste0(sn), "\n", filterRes)
14: (function (fs, pp_res, gFunc, popAlias, channels, gFunc_args)
{
require(openCyto)
sn <- sampleNames(fs)
fr <- as(fs, "flowFrame")
total <- nrow(fr)
subSample <- gFunc_args[["subSample"]]
gFunc_args[["subSample"]] <- NULL
if (!is.null(subSample)) {
if (is.numeric(subSample)) {
if (subSample > 1) {
samp.ind <- sample.int(total, subSample)
fr <- fr[samp.ind]
}
else if (subSample > 0) {
samp.ind <- sample.int(total, subSample * total)
fr <- fr[samp.ind]
}
else stop("invalid 'subSample' argument: ", subSample)
}
else stop("invalid 'subSample' argument: ", subSample)
}
openCyto.options <- getOption("openCyto")
minEvents <- openCyto.options[["gating"]][["minEvents"]]
if (is.null(minEvents))
minEvents <- 0
if (nrow(fr) <= minEvents) {
warning(paste(sn, collapse = ","), ": Not enough events to proceed the data-driven gating!Returning a dummy gate instead.")
channels <- as.vector(na.omit(channels))
nDim <- length(channels)
if (nDim == 1)
gate_coordinates <- list(c(-Inf, -Inf))
else if (nDim == 2)
gate_coordinates <- list(c(-Inf, -Inf), c(-Inf, -Inf))
else stop(nDim, " dimensional gating is not supported yet!")
names(gate_coordinates) <- channels
filterRes <- rectangleGate(gate_coordinates)
if (grepl("flowClust\\.[12]d", gFunc))
filterRes <- fcRectangleGate(filterRes, priors = list(),
posts = list())
nPop <- length(popAlias)
filterResType <- ifelse(nPop == 1, "filter", "filters")
if (filterResType == "filters") {
filterRes <- filters(lapply(1:nPop, function(i) filterRes))
}
}
else {
if (!.isRegistered(gFunc)) {
stop(sprintf("Can't gate using unregistered method %s",
gFunc))
}
thisCall <- substitute(f(fr = fr, pp_res = pp_res, channels = channels),
list(f = as.symbol(gFunc)))
filterRes <- try(do.call(gFunc, c(list(fr = fr, pp_res = pp_res,
channels = channels), gFunc_args)), silent = TRUE)
}
if (extends(class(filterRes), "filter") || extends(class(filterRes),
"filters")) {
list(sapply(sampleNames(fs), function(i) filterRes, simplify = FALSE))
}
else {
stop("failed at ", paste0(sn), "\n", filterRes)
}
})(dots[[1L]][[1L]], dots[[2L]][[1L]], gFunc = ".tmix2DGate.wrapper",
popAlias = c("cd41", "cd42", "cd43"), channels = c("Green-E-582/15-A",
"Violet-C-670/30-A"), gFunc_args = list(K = 3, quantile = 0.6,
trans = 0))
13: mapply(list(`Alcina TregMAIT_AV 10-1974 P1.fcs` = <S4 object of class "flowSet">,
`Alcina TregMAIT_BV 08-1966.fcs` = <S4 object of class "flowSet">,
`Alcina TregMAIT_CM 06-1955.fcs` = <S4 object of class "flowSet">,
`Alcina TregMAIT_GG 08-1951.fcs` = <S4 object of class "flowSet">,
`Alcina TregMAIT_LM 04-1938 P1.fcs` = <S4 object of class "flowSet">,
`Alcina TregMAIT_RM 01-1951.fcs` = <S4 object of class "flowSet">,
`Alcina TregMAIT_TA 09-1949 P1.fcs` = <S4 object of class "flowSet">),
list(`Alcina TregMAIT_AV 10-1974 P1.fcs` = NULL, `Alcina TregMAIT_BV 08-1966.fcs` = NULL,
`Alcina TregMAIT_CM 06-1955.fcs` = NULL, `Alcina TregMAIT_GG 08-1951.fcs` = NULL,
`Alcina TregMAIT_LM 04-1938 P1.fcs` = NULL, `Alcina TregMAIT_RM 01-1951.fcs` = NULL,
`Alcina TregMAIT_TA 09-1949 P1.fcs` = NULL), FUN = .gating_adaptor,
MoreArgs = list(gFunc = ".tmix2DGate.wrapper", popAlias = c("cd41",
"cd42", "cd43"), channels = c("Green-E-582/15-A", "Violet-C-670/30-A"
), gFunc_args = list(K = 3, quantile = 0.6, trans = 0)))
12: eval(expr, envir, enclos)
11: eval(thisCall)
10: .gating_gtMethod(x, y, ...)
9: gating(x = this_gate, y, parent = parent, gtPop = gt_node_pop,
pp_res = pp_res, ...)
8: gating(x = this_gate, y, parent = parent, gtPop = gt_node_pop,
pp_res = pp_res, ...)
7: .gating_gatingTemplate(x, y, env_fct, ...)
6: .local(x, y, ...)
5: gating(gt, gs, ...)
4: gating(gt, gs, ...)
3: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
2: suppressMessages(gating(gt, gs, ...))
1: add_pop(gs, alias = "cd41,cd42,cd43", pop = "*", parent = "root",
dims = "CD25,CD127", gating_method = "tmix2DGate.wrapper",
gating_args = "K = 3, quantile = 0.6, trans = 0")
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)
Sessioninfo()
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_1.12.0 flowClust_3.10.1 clue_0.3-51
[4] corpcor_1.6.8 mnormt_1.5-4 ellipse_0.3-8
[7] RBGL_1.48.1 graph_1.50.0 Biobase_2.32.0
[10] BiocGenerics_0.18.0 rgl_0.95.1441 flowIncubator_0.99.9
[13] ggplot2_2.1.0 data.table_1.9.6 flowStats_3.30.1
[16] cluster_2.0.4 fda_2.4.4 Matrix_1.2-6
[19] flowWorkspaceData_2.8.0 openCyto_1.10.3 flowWorkspace_3.18.8
[22] gridExtra_2.2.1 ncdfFlow_2.18.0 BH_1.60.0-2
[25] RcppArmadillo_0.7.100.3.1 flowViz_1.36.2 lattice_0.20-33
[28] flowCore_1.38.2
Could it also be due to the RStudio version that I have? They suggest updating the RStudio, however I have the newest one for Mac.