runSCENIC_3_scoreCells Error

[Conorisco]

As far as I can see this error doesn't appear in any other issue reported

When running runSCENIC_3_scoreCells() I get an error

Error in par(plt = gridPLT(), new = TRUE) : invalid value specified for graphical parameter "plt"

I have Scenic version 1.1.2-01 and newest version of GridExtra. Just wondering if anyone has any Idea what might be the issue?

R version 3.6.0 (2019-04-26) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] gridBase_0.4-7 RColorBrewer_1.1-2 data.table_1.12.2 doRNG_1.7.1 rngtools_1.4 pkgmaker_0.27 registry_0.5-1
[8] foreach_1.4.7 scater_1.12.2 ggplot2_3.2.1 SingleCellExperiment_1.6.0 SummarizedExperiment_1.14.0 DelayedArray_0.10.0 BiocParallel_1.18.0
[15] matrixStats_0.54.0 Biobase_2.44.0 GenomicRanges_1.36.0 GenomeInfoDb_1.20.0 IRanges_2.18.1 S4Vectors_0.22.0 BiocGenerics_0.30.0
[22] SCopeLoomR_0.5.0 RcisTarget_1.4.0 AUCell_1.6.1 SCENIC_1.1.2-01

loaded via a namespace (and not attached): [1] ggbeeswarm_0.6.0 colorspace_1.4-1 dynamicTreeCut_1.63-1 XVector_0.24.0 base64enc_0.1-3 BiocNeighbors_1.2.0 rstudioapi_0.10 DT_0.8
[9] bit64_0.9-7 AnnotationDbi_1.46.0 feather_0.3.4 codetools_0.2-16 R.methodsS3_1.7.1 doParallel_1.0.15 knitr_1.24 zeallot_0.1.0
[17] jsonlite_1.6 doMC_1.3.6 annotate_1.62.0 cluster_2.1.0 R.oo_1.22.0 pheatmap_1.0.12 graph_1.62.0 shiny_1.3.2
[25] compiler_3.6.0 backports_1.1.4 assertthat_0.2.1 Matrix_1.2-17 lazyeval_0.2.2 cli_1.1.0 later_0.8.0 BiocSingular_1.0.0
[33] htmltools_0.3.6 tools_3.6.0 rsvd_1.0.2 gtable_0.3.0 glue_1.3.1 GenomeInfoDbData_1.2.1 reshape2_1.4.3 dplyr_0.8.3
[41] Rcpp_1.0.2 NMF_0.21.0 vctrs_0.2.0 iterators_1.0.12 crosstalk_1.0.0 DelayedMatrixStats_1.6.0 xfun_0.9 stringr_1.4.0
[49] mime_0.7 irlba_2.3.3 XML_3.98-1.20 zlibbioc_1.30.0 zoo_1.8-6 scales_1.0.0 hms_0.5.1 promises_1.0.1
[57] yaml_2.2.0 memoise_1.1.0 gridExtra_2.3 stringi_1.4.3 RSQLite_2.1.2 bibtex_0.4.2 rlang_0.4.0 pkgconfig_2.0.2
[65] GENIE3_1.6.0 bitops_1.0-6 evaluate_0.14 lattice_0.20-38 purrr_0.3.2 htmlwidgets_1.3 bit_1.1-14 tidyselect_0.2.5
[73] GSEABase_1.46.0 plyr_1.8.4 magrittr_1.5 R6_2.4.0 DBI_1.0.0 pillar_1.4.2 withr_2.1.2 RCurl_1.95-4.12
[81] tibble_2.1.3 crayon_1.3.4 hdf5r_1.2.0 rmarkdown_1.15 viridis_0.5.1 grid_3.6.0 blob_1.2.0 digest_0.6.20
[89] xtable_1.8-4 httpuv_1.5.1 R.utils_2.9.0 munsell_0.5.0 beeswarm_0.2.3 viridisLite_0.3.0 vipor_0.4.5 sessioninfo_1.1.1

[liaoshengyou]

who can slove this problem? thanks

[fredust]

Hello, I am not sure whether you have solved the problem. I found that If you try to modify the cellinfo file to keep only cell cluster, study groups information, the problem will be solved.

[liaoshengyou]

yes, you are right....

[alisyedraza1]

Hello. What modifications did you make in the cellinfo file? Thanks.