Hi,
I have been using EGSEA and I very much like it. While everything works just fine, I do have an issue with heat map generation. For both the test data set (built-in) and for my very own data set I do not get any run time error but do not get any heat maps generated either. Although I do see the legends written out for each of the gene set. When I tried plotting it using the S4 result however, I got an error as follows -
> plotHeatmap(gsa)
ERROR: plotHeatmap(...) encountered an error:
Error in paste0("Generating heatmap for ", gene.set, " from the collection \n", : argument "gene.set" is missing, with no default
I am not sure where to find the gene.set variable. I would greatly appreciate your help.
Please find attached my Session info. Thanks, RV
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rgraphviz_2.20.0 RColorBrewer_1.1-2 data.table_1.10.4 reshape2_1.4.2 EGSEA_1.4.1 pathview_1.16.5 org.Hs.eg.db_3.4.1
[8] topGO_2.28.0 SparseM_1.77 GO.db_3.4.1 graph_1.54.0 AnnotationDbi_1.38.1 IRanges_2.10.2 S4Vectors_0.14.3
[15] gage_2.26.1 Biobase_2.36.2 BiocGenerics_0.22.0 edgeR_3.18.1 limma_3.32.3
loaded via a namespace (and not attached):
[1] nlme_3.1-131 bitops_1.0-6 matrixStats_0.52.2 GSVA_1.24.1 R2HTML_2.3.2 bit64_0.9-7
[7] httr_1.2.1 tools_3.4.0 doRNG_1.6.6 R6_2.2.2 KernSmooth_2.23-15 DBI_0.7
[13] lazyeval_0.2.0 colorspace_1.3-2 bit_1.1-12 compiler_3.4.0 pkgmaker_0.22 labeling_0.3
[19] caTools_1.17.1 KEGGgraph_1.38.1 scales_0.4.1 PADOG_1.18.0 stringr_1.2.0 digest_0.6.12
[25] XVector_0.16.0 pkgconfig_2.0.1 HTMLUtils_0.1.7 rlang_0.1.2 RSQLite_2.0 hwriter_1.3.2
[31] gtools_3.5.0 RCurl_1.95-4.8 magrittr_1.5 KEGG.db_3.2.3 Matrix_1.2-10 Rcpp_0.12.12
[37] munsell_0.4.3 stringi_1.1.5 zlibbioc_1.22.0 gplots_3.0.1 KEGGdzPathwaysGEO_1.14.0 plyr_1.8.4
[43] globaltest_5.30.0 blob_1.1.0 gdata_2.18.0 lattice_0.20-35 Biostrings_2.44.2 splines_3.4.0
[49] annotate_1.54.0 KEGGREST_1.16.1 locfit_1.5-9.1 hgu133plus2.db_3.2.3 hgu133a.db_3.2.3 rngtools_1.2.4
[55] EGSEAdata_1.4.0 codetools_0.2-15 XML_3.98-1.9 GSA_1.03 metap_0.8 png_0.1-7
[61] foreach_1.4.3 org.Mm.eg.db_3.4.1 gtable_0.2.0 org.Rn.eg.db_3.4.1 ggplot2_2.2.1 xtable_1.8-2
[67] survival_2.41-3 tibble_1.3.3 iterators_1.0.8 registry_0.3 memoise_1.1.0 safe_3.16.0
[73] GSEABase_1.38.0
