tsierocinski
commented
3 years ago after reading this: https://github.com/RGLab/openCyto/issues/194 and poking around
I realize that the problem, for both issues, also stems from the line
gtFile <- system.file("basic_gating.csv", package = "openCyto")
which returns an empty path. Using
dtTemplate <- fread("basic_gating.csv")
does the trick.
I think the unnecessary complication of using 'system.file' should be removed from the introduction tutorial - to avoid additional steps and confusion
jeffcraggy
Hi There,
I know this issue has been raised before but I cannot figure out what is wrong with my gating template.
here is the issue, I experience: ` rm(list=ls()) setwd("/data/") library(openCyto) library(flowWorkspace) library(ggcyto) library(data.table)
fcsFiles <- list.files(path="test/", pattern=".*fcs", full.names=T) fcs <- load_cytoset_from_fcs(fcsFiles)
gtFile <- system.file("basic_gating.csv", package = "openCyto") dtTemplate <- fread(gtFile) Error in fread(gtFile) : Input is empty or only contains BOM or terminal control characters
`
session Info:
`
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] data.table_1.14.0 ggcyto_1.20.0 ncdfFlow_2.38.0
[4] BH_1.75.0-0 RcppArmadillo_0.10.5.0.0 flowCore_2.4.0
[7] ggplot2_3.3.3 flowWorkspace_4.4.0 openCyto_2.4.0
loaded via a namespace (and not attached): [1] bitops_1.0-7 matrixStats_0.59.0 RColorBrewer_1.1-2
[4] httr_1.4.2 Rgraphviz_2.36.0 tools_4.1.0
[7] utf8_1.2.1 R6_2.5.0 KernSmooth_2.23-18
[10] DBI_1.1.1 BiocGenerics_0.38.0 colorspace_2.0-1
[13] withr_2.4.2 gridExtra_2.3 tidyselect_1.1.1
[16] mnormt_2.0.2 curl_4.3.1 compiler_4.1.0
[19] graph_1.70.0 Biobase_2.52.0 flowClust_3.30.0
[22] xml2_1.3.2 DelayedArray_0.18.0 labeling_0.4.2
[25] flowStats_4.4.0 scales_1.1.1 DEoptimR_1.0-9
[28] hexbin_1.28.2 mvtnorm_1.1-2 robustbase_0.93-8
[31] RBGL_1.68.0 digest_0.6.27 rainbow_3.6
[34] R.utils_2.10.1 rrcov_1.5-5 base64enc_0.1-3
[37] jpeg_0.1-8.1 pkgconfig_2.0.3 MatrixGenerics_1.4.0 [40] rlang_0.4.11 farver_2.1.0 generics_0.1.0
[43] mclust_5.4.7 gtools_3.9.2 dplyr_1.0.6
[46] R.oo_1.24.0 RCurl_1.98-1.3 magrittr_2.0.1
[49] RProtoBufLib_2.4.0 Matrix_1.3-2 Rcpp_1.0.6
[52] munsell_0.5.0 S4Vectors_0.30.0 fansi_0.5.0
[55] lifecycle_1.0.0 R.methodsS3_1.8.1 MASS_7.3-53.1
[58] zlibbioc_1.38.0 plyr_1.8.6 grid_4.1.0
[61] parallel_4.1.0 crayon_1.4.1 lattice_0.20-41
[64] splines_4.1.0 tmvnsim_1.0-2 pillar_1.6.1
[67] fda_5.1.9 corpcor_1.6.9 stats4_4.1.0
[70] XML_3.99-0.6 glue_1.4.2 latticeExtra_0.6-29 [73] RcppParallel_5.1.4 png_0.1-7 vctrs_0.3.8
[76] gtable_0.3.0 aws.s3_0.3.21 purrr_0.3.4
[79] clue_0.3-59 assertthat_0.2.1 ks_1.13.1
[82] fds_1.8 pracma_2.3.3 IDPmisc_1.1.20
[85] pcaPP_1.9-74 tibble_3.1.2 IRanges_2.26.0
[88] cytolib_2.4.0 aws.signature_0.6.0 flowViz_1.56.0
[91] ellipse_0.4.2 cluster_2.1.1 ellipsis_0.3.2
[94] hdrcde_3.4
`
basic_gating.csv template attached basic_gating.csv
Thanks for the help