Hi, I am getting the error below ("only 0's may be mixed with negative subscripts") on certain data sets during the report generation stage when running EGSEA. I believe it has to do with plotting certain KEGG pathways in pathview, as others have reported here: https://github.com/lgeistlinger/EnrichmentBrowser/issues/10. Do you have any suggestions to work around this problem? Or, if I am correct, do you have any plans to update your R package to handle this problem?
Thanks for your help.
> gsa = egsea(voom.results = v, contrasts = contr.matrix, gs.annots = gs.annots, baseGSEAs = egsea.base(), symbolsMap = v$genes, sort.by = "med.rank", num.threads = 4, report = TRUE) EGSEA analysis has started ##------ Fri Jun 21 14:52:26 2019 ------## Log fold changes are estimated using limma package ... limma DE analysis is carried out ... EGSEA is running on the provided data and c2 collection EGSEA is running on the provided data and c3 collection EGSEA is running on the provided data and c5 collection EGSEA is running on the provided data and c7 collection EGSEA is running on the provided data and kegg collection ##------ Fri Jun 21 15:06:04 2019 ------## EGSEA analysis took 818.169 seconds. EGSEA analysis has completed EGSEA HTML report is being generated ... ##------ Fri Jun 21 15:06:04 2019 ------## Report pages and figures are being generated for the c2 collection ... Error in img[pidx[i, 3]:pidx[i, 4], sel.px, 1:3] : only 0's may be mixed with negative subscripts
From my session info, you can see that I am working on a new computer with the newest installation of R and EGSEA:
> sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.5 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:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  grid parallel stats4 stats graphics grDevices utils datasets  methods base other attached packages:  Rgraphviz_2.28.0 edgeR_3.26.4 limma_3.40.2  EGSEAdata_1.12.0 EGSEA_1.12.0 pathview_1.24.0  org.Hs.eg.db_3.8.2 topGO_2.36.0 SparseM_1.77  GO.db_3.8.2 graph_1.62.0 gage_2.34.0  RColorBrewer_1.1-2 pheatmap_1.0.12 ggplot2_3.2.0  org.Mm.eg.db_3.8.2 AnnotationDbi_1.46.0 DESeq2_1.24.0  SummarizedExperiment_1.14.0 DelayedArray_0.10.0 BiocParallel_1.18.0  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 loaded via a namespace (and not attached):  backports_1.1.4 Hmisc_4.2-0 lazyeval_0.2.2  GSEABase_1.46.0 splines_3.6.0 inline_0.3.15  digest_0.6.19 foreach_1.4.4 htmltools_0.3.6  gdata_2.18.0 magrittr_1.5 checkmate_1.9.3  memoise_1.1.0 cluster_2.0.9 Biostrings_2.52.0  org.Rn.eg.db_3.8.2 annotate_1.62.0 KEGGdzPathwaysGEO_1.22.0  prettyunits_1.0.2 colorspace_1.4-1 blob_1.1.1  xfun_0.7 dplyr_0.8.1 callr_3.2.0  crayon_1.3.4 RCurl_1.95-4.12 jsonlite_1.6  genefilter_1.66.0 survival_2.44-1.1 iterators_1.0.10  glue_1.3.1 registry_0.5-1 gtable_0.3.0  zlibbioc_1.30.0 XVector_0.24.0 R2HTML_2.3.2  hgu133a.db_3.2.3 pkgbuild_1.0.3 KEGG.db_3.2.3  rstan_2.18.2 scales_1.0.0 DBI_1.0.0  rngtools_22.214.171.124 bibtex_0.4.2 Rcpp_1.0.1  metap_1.1 viridisLite_0.3.0 xtable_1.8-4  htmlTable_1.13.1 foreign_0.8-71 bit_1.1-14  Formula_1.2-3 StanHeaders_2.18.1-10 GSVA_1.32.0  DT_0.7 htmlwidgets_1.3 httr_1.4.0  hgu133plus2.db_3.2.3 gplots_126.96.36.199 acepack_1.4.1  loo_2.1.0 pkgconfig_2.0.2 XML_3.98-1.20  nnet_7.3-12 locfit_1.5-9.1 tidyselect_0.2.5  labeling_0.3 rlang_0.3.4 later_0.8.0  munsell_0.5.0 tools_3.6.0 cli_1.1.0  RSQLite_2.1.1 globaltest_5.38.0 HTMLUtils_0.1.7  stringr_1.4.0 processx_3.3.1 knitr_1.23  bit64_0.9-7 caTools_188.8.131.52 purrr_0.3.2  KEGGREST_1.24.0 nlme_3.1-140 doRNG_1.7.1  mime_0.7 KEGGgraph_1.44.0 compiler_3.6.0  shinythemes_1.1.2 rstudioapi_0.10 curl_3.3  plotly_4.9.0 png_0.1-7 tibble_2.1.3  geneplotter_1.62.0 stringi_1.4.3 ps_1.3.0  Glimma_1.12.0 lattice_0.20-38 Matrix_1.2-17  pillar_1.4.1 GSA_1.03.1 Rdpack_0.11-0  PADOG_1.26.0 data.table_1.12.2 bitops_1.0-6  gbRd_0.4-11 httpuv_1.5.1 R6_2.4.0  latticeExtra_0.6-28 hwriter_1.3.2 promises_1.0.1  KernSmooth_2.23-15 gridExtra_2.3 codetools_0.2-16  gtools_3.8.1 assertthat_0.2.1 pkgmaker_0.27  safe_3.24.0 withr_2.1.2 GenomeInfoDbData_1.2.1  rpart_4.1-15 tidyr_0.8.3 shiny_1.3.2  base64enc_0.1-3