Hi Matt,
Great to see you again at BioC2016! And thanks so much for telling me about Glimma - the interactive visualizations are amazing and my clients will love them. I got the devel version to work yesterday but I was playing around with it this morning and found a problem - if you pass the anno argument a data.frame that has a column containing TRUE/FALSE values, nothing appears when you open the HTML. Sorry I can't send a working example but you should be able to verify on your own. I switched the T/F to character "yes"/"no" and then the html showed the interactive plot.
Thanks again for a great addition to the limma/edgeR/DESeq2 analysis pipelines!
Jenny
sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] Glimma_1.1.3 org.Hs.eg.db_3.3.0 AnnotationDbi_1.35.3 rgl_0.95.1441 rtracklayer_1.33.8
[6] GenomicRanges_1.25.8 GenomeInfoDb_1.9.2 IRanges_2.7.11 S4Vectors_0.11.7 gplots_3.0.1
[11] magrittr_1.5 WGCNA_1.51 fastcluster_1.1.20 dynamicTreeCut_1.63-1 Biobase_2.33.0
[16] BiocGenerics_0.19.1 edgeR_3.15.0 limma_3.29.12
loaded via a namespace (and not attached):
[1] Category_2.39.0 bitops_1.0-6 matrixStats_0.50.2 doParallel_1.0.10
[5] RColorBrewer_1.1-2 httr_1.2.0 tools_3.3.1 R6_2.1.2
[9] KernSmooth_2.23-15 rpart_4.1-10 Hmisc_3.17-4 DBI_0.4-1
[13] colorspace_1.2-6 nnet_7.3-12 gridExtra_2.2.1 GGally_1.1.0
[17] DESeq2_1.13.6 preprocessCore_1.35.0 chron_2.3-47 graph_1.51.0
[21] ggbio_1.21.2 caTools_1.17.1 scales_0.4.0 genefilter_1.55.2
[25] RBGL_1.49.1 stringr_1.0.0 digest_0.6.9 Rsamtools_1.25.0
[29] foreign_0.8-66 R.utils_2.3.0 AnnotationForge_1.15.4 XVector_0.13.2
[33] dichromat_2.0-0 htmltools_0.3.5 ensembldb_1.5.8 BSgenome_1.41.2
[37] impute_1.47.0 PFAM.db_3.3.0 RSQLite_1.0.0 BiocInstaller_1.23.4
[41] shiny_0.13.2 GOstats_2.39.1 gtools_3.5.0 BiocParallel_1.7.4
[45] acepack_1.3-3.3 R.oo_1.20.0 VariantAnnotation_1.19.4 RCurl_1.95-4.8
[49] GO.db_3.3.0 Formula_1.2-1 Matrix_1.2-6 Rcpp_0.12.5
[53] munsell_0.4.3 R.methodsS3_1.7.1 stringi_1.1.1 SummarizedExperiment_1.3.6
[57] zlibbioc_1.19.0 plyr_1.8.4 AnnotationHub_2.5.4 grid_3.3.1
[61] gdata_2.17.0 lattice_0.20-33 Biostrings_2.41.4 splines_3.3.1
[65] GenomicFeatures_1.25.14 annotate_1.51.0 locfit_1.5-9.1 knitr_1.13
[69] geneplotter_1.51.0 reshape2_1.4.1 codetools_0.2-14 biomaRt_2.29.2
[73] XML_3.98-1.4 biovizBase_1.21.0 latticeExtra_0.6-28 data.table_1.9.6
[77] httpuv_1.3.3 foreach_1.4.3 gtable_0.2.0 reshape_0.8.5
[81] ggplot2_2.1.0 mime_0.4 xtable_1.8-2 survival_2.39-5
[85] OrganismDbi_1.15.1 iterators_1.0.8 GenomicAlignments_1.9.4 cluster_2.0.4
[89] interactiveDisplayBase_1.11.3 GSEABase_1.35.0
