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DillonHammill / CytoExploreR

Interactive Cytometry Data Analysis
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cyto_map not working #203

Open bvoneyss opened 2 months ago

bvoneyss commented 2 months ago

Describe the bug Hi, I recently started using CytoExploreR, and I really love this package!! Thx a lot!

When I run cyto_map on a GatingSet object (gs) cyto_map returns the following error:

 cyto_map(
    gs,
    #parent = "LSK", # population to map
    channels = c("CD48","CD34"),
    display = 1000
)

Computing UMAP co-ordinates... Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 5 did not have 3 elements

All other functions I have tested so far (cyto_gate_draw, cyto_gate_copy, cyto_copy, cyto_plot_gating_scheme, cyto_stats_compute) work perfectly fine with this object but cyto_map keeps returning this error.

To Reproduce see above

Expected behavior normally cyto_map should return a dimensionality reduction plot (here UMAP).

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information): R Studio server on Linux: Operating System: SUSE Linux Enterprise Server 15 SP5 CPE OS Name: cpe:/o:suse:sles:15:sp5 Kernel: Linux 5.14.21-150500.55.52-default

sessionInfo() other attached packages: [1] RColorBrewer_1.1-3 flowSpecs_1.16.0 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[8] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 tidyverse_2.0.0 ggpubr_0.6.0 ggplot2_3.5.0 ncdfFlow_2.48.0
[15] BH_1.84.0-0 CytoExploreRData_1.0.3 CytoExploreR_1.1.0 openCyto_2.14.0 flowCore_2.14.2 flowWorkspace_4.14.3

Additional context Add any other context about the problem here.

djhammill commented 1 month ago

Pasting the output of traceback() here after you get the error may be informative.

bvoneyss commented 1 month ago

Sorry. Here is the output of traceback()

traceback() 10: scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul) 9: read.table(filename, sep = sep, header = header, quote = quote, stringsAsFactors = stringsAsFactors, row.names = row.names, comment.char = varMetadata.char, ...) 8: read.AnnotatedDataFrame(file.path(path, phenoData), header = TRUE, sep = sep, as.is = as.is, colClasses = c(FCS_File = "character"), ...) 7: flowCore:::parse_pd_for_read_fs(files, path, pattern, phenoData, sep, as.is, file_col_name = file_col_name, ...) 6: load_cytoset_from_fcs(phenoData = list.files(tmp, pattern = ".txt"), path = tmp, backend = backend, backend_dir = path, file_col_name = "FCS_File", check.names = FALSE, ...) 5: flowSet_to_cytoset(flowSet(cyto_data)) 4: FUN(X[[i]], ...) 3: lapply(seq_along(gs_list), function(z) { gs <- gs_list[[z]] fs <- cyto_extract(gs, parent = parent) fr <- cyto_merge_by(fs, merge_by = "all")[[1]] cyto_data <- cyto_map(fr, channels = channels, display = display, type = type, split = split, names = names[[z]], save_as = save_as, inverse = inverse, trans = trans, plot = FALSE, seed = seed, cyto_map_fun = cyto_map_fun, ...) cyto_data <- cyto_split(cyto_data, names = names[[z]]) return(flowSet_to_cytoset(flowSet(cyto_data))) }) 2: cyto_map.GatingSet(gs, type = uwot::umap, display = 1000) 1: cyto_map(gs, type = uwot::umap, display = 1000)

Thx, Björn

On 4. Jun 2024, at 03:21, Dillon Hammill @.***> wrote:

Pasting the output of traceback() here after you get the error may be informative.

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