Heatmap issues input is not a matrix, it should be a simple vector #27
Description
`hsamsi<-buildMSIGDB(species="human",keytype = "SYMBOL",anntype = "REACTOME")
res_reactome <- scgsva(groupA_DCC,hsamsi,method="ssgsea", maxRank=2000, cores = 6)
featurePlot(res_reactome,features = c("EUKARYOTIC_TRANSLATION_INITIATION"), group_by = "sample")
Heatmap(res_reactome)
Error: If input is not a matrix, it should be a simple vector.`
After building the reactome database and running scgsva, I get results that run with featureplot, ridgeplot, but I get errors for Heatmap.
Any suggestions?
`> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.utf8 LC_CTYPE=English_Canada.utf8 LC_MONETARY=English_Canada.utf8
[4] LC_NUMERIC=C LC_TIME=English_Canada.utf8
time zone: America/Vancouver
tzcode source: internal
attached base packages:
[1] stats4 grid stats graphics grDevices datasets utils methods base
other attached packages:
[1] data.table_1.15.4 DT_0.33 pheatmap_1.0.12 EnhancedVolcano_1.20.0
[5] ggrepel_0.9.5 devtools_2.4.5 usethis_2.2.3 remotes_2.5.0
[9] BiocManager_1.30.22 cowplot_1.1.3 monocle3_1.3.7 SingleCellExperiment_1.24.0
[13] SummarizedExperiment_1.32.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 IRanges_2.36.0
[17] S4Vectors_0.40.2 MatrixGenerics_1.14.0 matrixStats_1.3.0 Biobase_2.62.0
[21] BiocGenerics_0.48.1 SeuratWrappers_0.3.5 fgsea_1.28.0 UCell_2.6.2
[25] jsonlite_1.8.8 writexl_1.5.0 here_1.0.1 BiocParallel_1.36.0
[29] knitr_1.46 glue_1.7.0 limma_3.58.1 igraph_2.0.3
[33] viridis_0.6.5 viridisLite_0.4.2 clustree_0.5.1 ggraph_2.2.1
[37] RColorBrewer_1.1-3 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[41] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[45] ggplot2_3.5.1 tidyverse_2.0.0 dplyr_1.1.4 Seurat_5.0.3
[49] msigdbr_7.5.1 ComplexHeatmap_2.15.4 SeuratObject_5.0.1 scGSVA_0.0.22
loaded via a namespace (and not attached):
[1] fs_1.6.4 GSVA_1.50.5 spatstat.sparse_3.0-3 bitops_1.0-7
[5] httr_1.4.7 doParallel_1.0.17 profvis_0.3.8 tools_4.3.1
[9] sctransform_0.4.1 backports_1.4.1 utf8_1.2.4 R6_2.5.1
[13] HDF5Array_1.30.1 lazyeval_0.2.2 uwot_0.2.2 rhdf5filters_1.14.1
[17] GetoptLong_1.0.5 urlchecker_1.0.1 withr_3.0.0 sp_2.1-3
[21] gridExtra_2.3 progressr_0.14.0 cli_3.6.2 spatstat.explore_3.2-7
[25] fastDummies_1.7.3 labeling_0.4.3 spatstat.data_3.0-4 ggridges_0.5.6
[29] pbapply_1.7-2 R.utils_2.12.3 sessioninfo_1.2.2 parallelly_1.37.1
[33] rstudioapi_0.16.0 RSQLite_2.3.6 generics_0.1.3 shape_1.4.6.1
[37] ica_1.0-3 spatstat.random_3.2-3 car_3.1-2 Matrix_1.6-5
[41] fansi_1.0.6 abind_1.4-5 R.methodsS3_1.8.2 lifecycle_1.0.4
[45] carData_3.0-5 rhdf5_2.46.1 SparseArray_1.2.4 Rtsne_0.17
[49] blob_1.2.4 promises_1.3.0 crayon_1.5.2 miniUI_0.1.1.1
[53] lattice_0.21-8 beachmat_2.18.1 annotate_1.80.0 KEGGREST_1.42.0
[57] pillar_1.9.0 boot_1.3-28.1 rjson_0.2.21 future.apply_1.11.2
[61] codetools_0.2-19 fastmatch_1.1-4 leiden_0.4.3.1 vctrs_0.6.5
[65] png_0.1-8 spam_2.10-0 gtable_0.3.5 cachem_1.0.8
[69] xfun_0.43 S4Arrays_1.2.1 mime_0.12 tidygraph_1.3.1
[73] survival_3.5-5 iterators_1.0.14 statmod_1.5.0 ellipsis_0.3.2
[77] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-162 bit64_4.0.5
[81] RcppAnnoy_0.0.22 rprojroot_2.0.4 irlba_2.3.5.1 KernSmooth_2.23-21
[85] colorspace_2.1-0 DBI_1.2.2 processx_3.8.4 tidyselect_1.2.1
[89] curl_5.2.1 bit_4.0.5 compiler_4.3.1 graph_1.80.0
[93] BiocNeighbors_1.20.2 desc_1.4.3 DelayedArray_0.28.0 plotly_4.10.4
[97] scales_1.3.0 lmtest_0.9-40 callr_3.7.6 digest_0.6.35
[101] goftest_1.2-3 minqa_1.2.6 spatstat.utils_3.0-4 XVector_0.42.0
[105] htmltools_0.5.8.1 pkgconfig_2.0.3 lme4_1.1-35.3 sparseMatrixStats_1.14.0
[109] fastmap_1.1.1 rlang_1.1.3 GlobalOptions_0.1.2 htmlwidgets_1.6.4
[113] shiny_1.8.1.1 DelayedMatrixStats_1.24.0 farver_2.1.1 zoo_1.8-12
[117] R.oo_1.26.0 BiocSingular_1.18.0 RCurl_1.98-1.14 magrittr_2.0.3
[121] GenomeInfoDbData_1.2.11 dotCall64_1.1-1 patchwork_1.2.0 Rhdf5lib_1.24.2
[125] munsell_0.5.1 Rcpp_1.0.12 babelgene_22.9 reticulate_1.36.1
[129] stringi_1.8.3 zlibbioc_1.48.2 MASS_7.3-60 pkgbuild_1.4.4
[133] plyr_1.8.9 parallel_4.3.1 listenv_0.9.1 deldir_2.0-4
[137] Biostrings_2.70.3 graphlayouts_1.1.1 splines_4.3.1 tensor_1.5
[141] hms_1.1.3 circlize_0.4.16 ps_1.7.6 spatstat.geom_3.2-9
[145] RcppHNSW_0.6.0 pkgload_1.3.4 reshape2_1.4.4 ScaledMatrix_1.10.0
[149] XML_3.99-0.16.1 renv_1.0.7 nloptr_2.0.3 tzdb_0.4.0
[153] foreach_1.5.2 tweenr_2.0.3 httpuv_1.6.15 RANN_2.6.1
[157] polyclip_1.10-6 future_1.33.2 clue_0.3-65 scattermore_1.2
[161] ggforce_0.4.2 rsvd_1.0.5 broom_1.0.5 xtable_1.8-4
[165] RSpectra_0.16-1 rstatix_0.7.2 later_1.3.2 memoise_2.0.1
[169] AnnotationDbi_1.64.1 cluster_2.1.4 timechange_0.3.0 globals_0.16.3
[173] GSEABase_1.64.0 `