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Hi, I'm having trouble adding an annotation column to my heatmap. My heatmap does not show the annotation column. Can you tell me what might be the problem? This is an example code:
sce <- mockSCE()
sce <- logNormCounts(sce)
plotHeatmap(sce[1:10,1:10], features=rownames(sce)[1:10],
colour_columns_by="Cell_Cycle", center=TRUE)
This works fine for me. Can you post your
sessionInfo()?R version 4.2.1 (2022-06-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Rocky Linux 8.7 (Green Obsidian)
Matrix products: default BLAS/LAPACK: /g/easybuild/x86_64/Rocky/8/haswell/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64/libflexiblas.so.3.2
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
[9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] iSEEu_1.8.0 shiny_1.7.1 iSEE_2.8.0 GGally_2.1.2 igraph_1.3.2
[6] NewWave_1.6.0 scry_1.8.0 deMULTIplex2_1.0.1 MESS_0.5.9 DEsingle_1.16.0
[11] org.Hs.eg.db_3.15.0 AnnotationDbi_1.58.0 progeny_1.18.0 ggraph_2.0.5 Neighborseq_0.1.0
[16] apeglm_1.18.0 glmGamPoi_1.8.0 plotly_4.10.1 batchelor_1.12.3 pheatmap_1.0.12
[21] MAST_1.22.0 ggrepel_0.9.1 NMF_0.25 bigmemory_4.6.1 cluster_2.1.3
[26] rngtools_1.5.2 registry_0.5-1 data.table_1.14.2 msigdbr_7.5.1 SingleR_1.10.0
[31] celldex_1.6.0 writexl_1.4.0 bluster_1.6.0 scDblFinder_1.10.0 scran_1.24.1
[36] scater_1.24.0 scuttle_1.6.3 SingleCellExperiment_1.18.1 umap_0.2.9.0 reticulate_1.26
[41] deMULTIplex_1.0.2 SeuratObject_4.1.3 Seurat_4.2.1 limma_3.52.2 forcats_0.5.1
[46] stringr_1.5.0 dplyr_1.1.2 purrr_1.0.1 readr_2.1.2 tidyr_1.3.0
[51] tibble_3.2.1 tidyverse_1.3.1 RColorBrewer_1.1-3 xlsx_0.6.5 readxl_1.4.0
[56] rstatix_0.7.0 ggpubr_0.4.0 ggplot2_3.4.2 clusterProfiler_4.4.4 DESeq2_1.36.0
[61] SummarizedExperiment_1.26.1 Biobase_2.56.0 MatrixGenerics_1.8.1 matrixStats_0.62.0 GenomicRanges_1.48.0
[66] GenomeInfoDb_1.32.2 IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0
loaded via a namespace (and not attached): [1] graphlayouts_0.8.0 pbapply_1.5-0 lattice_0.20-45 rJava_1.0-6
[5] haven_2.5.0 vctrs_0.6.2 rintrojs_0.3.2 mgcv_1.8-40
[9] blob_1.2.3 survival_3.3-1 spatstat.data_3.0-0 later_1.3.0
[13] DBI_1.1.3 rappdirs_0.3.3 uwot_0.1.14 dqrng_0.3.0
[17] jpeg_0.1-9 zlibbioc_1.42.0 GlobalOptions_0.1.2 htmlwidgets_1.5.4
[21] mvtnorm_1.1-3 future_1.26.1 miscTools_0.6-26 leiden_0.4.2
[25] parallel_4.2.1 irlba_2.3.5 tidygraph_1.2.1 Rcpp_1.0.8.3
[29] KernSmooth_2.23-20 DT_0.23 promises_1.2.0.1 DelayedArray_0.22.0
[33] ShortRead_1.54.0 RSpectra_0.16-1 fs_1.5.2 fastmatch_1.1-3
[37] mnormt_2.1.0 digest_0.6.29 png_0.1-7 sctransform_0.3.5
[41] scatterpie_0.1.7 cowplot_1.1.1 DOSE_3.22.0 pkgconfig_2.0.3
[45] GO.db_3.15.0 gridBase_0.4-7 spatstat.random_3.0-1 ggnewscale_0.4.7
[49] DelayedMatrixStats_1.18.0 ggbeeswarm_0.6.0 iterators_1.0.14 emdbook_1.3.12
[53] circlize_0.4.15 beeswarm_0.4.0 bslib_0.3.1 GetoptLong_1.0.5
[57] xfun_0.31 zoo_1.8-10 tidyselect_1.2.0 reshape2_1.4.4
[61] ica_1.0-2 labelled_2.9.1 viridisLite_0.4.0 rtracklayer_1.56.1
[65] rlang_1.1.1 jquerylib_0.1.4 ggformula_0.10.1 glue_1.6.2
[69] metap_1.8 modelr_0.1.8 ggsignif_0.6.3 mutoss_0.1-12
[73] httpuv_1.6.5 BiocNeighbors_1.14.0 TH.data_1.1-1 DO.db_2.9
[77] annotate_1.74.0 jsonlite_1.8.4 XVector_0.36.0 bit_4.0.4
[81] mime_0.12 gridExtra_2.3 Rsamtools_2.12.0 stringi_1.7.6
[85] spatstat.sparse_3.0-0 scattermore_0.8 spatstat.explore_3.0-3 rbibutils_2.2.8
[89] yulab.utils_0.0.5 bitops_1.0-7 cli_3.6.1 Rdpack_2.3.1
[93] RSQLite_2.2.14 bigmemory.sri_0.1.3 rstudioapi_0.14 GenomicAlignments_1.32.0
[97] nlme_3.1-158 qvalue_2.28.0 locfit_1.5-9.5 listenv_0.8.0
[101] miniUI_0.1.1.1 gridGraphics_0.5-1 dbplyr_2.3.2 lifecycle_1.0.3
[105] mosaicCore_0.9.0 ExperimentHub_2.4.0 munsell_0.5.0 cellranger_1.1.0
[109] hwriter_1.3.2.1 codetools_0.2-18 coda_0.19-4 vipor_0.4.5
[113] lmtest_0.9-40 shinyWidgets_0.7.0 xlsxjars_0.6.1 xtable_1.8-4
[117] ROCR_1.0-11 BiocManager_1.30.18 abind_1.4-5 farver_2.1.0
[121] parallelly_1.32.0 ResidualMatrix_1.6.0 ggExtra_0.10.0 AnnotationHub_3.4.0
[125] RANN_2.6.1 aplot_0.1.6 askpass_1.1 ggtree_3.4.1
[129] BiocIO_1.6.0 RcppAnnoy_0.0.19 goftest_1.2-3 patchwork_1.1.2
[133] future.apply_1.9.0 Matrix_1.5-1 tidytree_0.3.9 ellipsis_0.3.2
[137] shinydashboard_0.7.2 lubridate_1.8.0 ggridges_0.5.3 reprex_2.0.1
[141] multtest_2.52.0 ggstance_0.3.5 fgsea_1.22.0 shinyjs_2.1.0
[145] TFisher_0.2.0 spatstat.utils_3.0-1 htmltools_0.5.2 BiocFileCache_2.4.0
[149] yaml_2.3.5 utf8_1.2.2 interactiveDisplayBase_1.34.0 XML_3.99-0.10
[153] withr_2.5.0 fitdistrplus_1.1-8 BiocParallel_1.30.4 bit64_4.0.5
[157] xgboost_1.6.0.1 multiROC_1.1.1 multcomp_1.4-19 foreach_1.5.2
[161] Biostrings_2.64.0 progressr_0.10.1 GOSemSim_2.22.0 rsvd_1.0.5
[165] ScaledMatrix_1.4.0 evaluate_0.15 memoise_2.0.1 VGAM_1.1-6
[169] geepack_1.3.4 geneplotter_1.74.0 tzdb_0.3.0 gamlss.data_6.0-2
[173] gamlss_5.4-3 curl_4.3.2 qqconf_1.2.3 fansi_1.0.3
[177] tensor_1.5 edgeR_3.38.1 cachem_1.0.6 deldir_1.0-6
[181] maxLik_1.5-2 babelgene_22.3 metapod_1.4.0 rjson_0.2.21
[185] clue_0.3-61 tools_4.2.1 sass_0.4.1 sandwich_3.0-2
[189] magrittr_2.0.3 RCurl_1.98-1.7 car_3.1-0 ape_5.6-2
[193] ggplotify_0.1.0 xml2_1.3.3 rmarkdown_2.14 httr_1.4.6
[197] boot_1.3-28 globals_0.15.0 R6_2.5.1 stringdist_0.9.8
[201] genefilter_1.78.0 KEGGREST_1.36.2 treeio_1.20.1 shape_1.4.6
[205] gtools_3.9.2.2 statmod_1.4.36 beachmat_2.12.0 BiocVersion_3.15.2
[209] BiocSingular_1.12.0 splines_4.2.1 carData_3.0-5 ggfun_0.0.6
[213] colorspace_2.0-3 generics_0.1.2 pillar_1.9.0 sn_2.0.2
[217] tweenr_1.0.2 sp_1.5-1 uuid_1.1-0 GenomeInfoDbData_1.2.8
[221] plyr_1.8.7 gtable_0.3.0 bdsmatrix_1.3-6 rvest_1.0.2
[225] colourpicker_1.1.1 restfulr_0.0.15 ComplexHeatmap_2.12.0 latticeExtra_0.6-29
[229] knitr_1.39 gamlss.dist_6.0-3 shadowtext_0.1.2 fastmap_1.1.0
[233] pscl_1.5.5 doParallel_1.0.17 broom_1.0.4 SharedObject_1.10.0
[237] openssl_2.0.2 scales_1.2.0 filelock_1.0.2 backports_1.4.1
[241] plotrix_3.8-2 enrichplot_1.16.2 hms_1.1.1 ggforce_0.3.3
[245] Rtsne_0.16 polyclip_1.10-0 grid_4.2.1 numDeriv_2016.8-1.1
[249] mathjaxr_1.6-0 bbmle_1.0.25 lazyeval_0.2.2 geeM_0.10.1
[253] crayon_1.5.1 shinyAce_0.4.2 MASS_7.3-57 downloader_0.4
[257] sparseMatrixStats_1.8.0 reshape_0.8.9 viridis_0.6.2 compiler_4.2.1
[261] spatstat.geom_3.0-3
You need to use
color_columns_byfor that version of scater, notcolour_columns_by.Awesome! Thank you!!