using flowIncubator package's function
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Entering edit mode
anara92 • 0
@anara92-10628
Last seen 5.3 years ago

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.

opencyto flow cytometry R package installation • 726 views
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Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 15 days ago
(Private Address)

flowIncubaor is not a bioconductor package, so let's keep the conversations on github instead

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