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I am not able to increase the size (height) of the column annotations of the heatmap. I tried annotation_height, height, and re_size but none of them seems to work.
df<-featuresFilt[,c("Tissue","New.Diagnosis","Age","Sex","Race","TumorSite")]
colnames(df)<-c("Tissue","Diagnosis","Age","Sex","Race","TumorSite")
ha = HeatmapAnnotation(
#df = features[,c(5,6,7,13,15)],
#df = featuresFilt[,c(3,4,5,6,13,7)],
df = df,
col = list(Tissue = col_tissue,
Diagnosis = col_disease,#c("Normal" = "black","Adrenocortical carcinoma" = "red"),#col_cluster,#c("Adrenocortical carcinoma" = "red", "Normal" = "black", "Carcinoid tumor" = "blue","Gastrointestinal stromal tumor"="brown"),
Age = col_age,
Sex = genderColor,#c("Male"="turquoise","Female"="brown"),
#RIN = col_rin,
Race =raceColor,#c("White"="#B35806","Unknown"="#FDBC6B","Other"="black","Black or African American"="#E3E4EF","Native Hawaiian or Other Pacific Islander"="#8D81B6","Asian"="blue"),
TumorSite=tumorSiteColor#c("Metastasis"="turquoise","Primary Site"="brown","Recurrence"="black")
#cluster = col_cluster
),
#annotation_height = unit(rep(6,6), "mm"),
#height = unit(36,"mm"),
#annotation_name_gp = gpar(fontsize = 14,fontface = 2),
#annotation_legend_param = list(title_gp = gpar(fontsize = 15, fontface = 2),labels_gp = gpar(fontsize = 12)),
#annotation_height = unit(rep(2,6), "cm"),
annotation_height = c(TumorSite = unit(8, "mm"),Diagnosis=unit(8, "mm"),Age=unit(8, "mm"),Sex=unit(8, "mm"),Race=unit(8, "mm"),TumorSite=unit(8, "mm")), height = unit(48, "mm")
)
print(ha)
A HeatmapAnnotation object with 6 annotations
name: heatmap_annotation_273
position: column
items: 47
width: 1npc
height: 31.757299017573mm
this object is subsetable
20.0161333333333mm extension on the right
name annotation_type color_mapping height
Tissue discrete vector user-defined 5mm
Diagnosis discrete vector user-defined 5mm
Age continuous vector user-defined 5mm
Sex discrete vector user-defined 5mm
Race discrete vector user-defined 5mm
TumorSite discrete vector user-defined 5mm
sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] RSQLite_2.2.7 dplyr_1.0.7 WGCNA_1.70-3 fastcluster_1.2.3 dynamicTreeCut_1.63-1 concaveman_1.1.0 ggforce_0.3.3
[8] ggnewscale_0.4.5 ggnetwork_0.5.10 ggplot2_3.3.5 igraph_1.2.6 fs_1.5.0 data.table_1.14.0 rrvgo_1.2.0
[15] randomcoloR_1.1.0.1 circlize_0.4.13 RColorBrewer_1.1-2 ComplexHeatmap_2.6.2 stringr_1.4.0 openxlsx_4.2.4 maftools_2.6.05
[22] ExperimentHub_1.16.1 AnnotationHub_2.22.1 BiocFileCache_1.14.0 dbplyr_2.1.1 BiocGenerics_0.36.1
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 R.methodsS3_1.8.1 ragg_1.1.3 tidyr_1.1.3 bit64_4.0.5
[6] knitr_1.33 DelayedArray_0.16.3 R.utils_2.10.1 rpart_4.1-15 RCurl_1.98-1.3
[11] doParallel_1.0.16 generics_0.1.0 preprocessCore_1.52.1 cowplot_1.1.1 chron_2.3-56
[16] bit_4.0.4 tzdb_0.1.2 xml2_1.3.2 lubridate_1.7.10 httpuv_1.6.1
[21] SummarizedExperiment_1.20.0 assertthat_0.2.1 STRINGdb_2.2.2 xfun_0.24 hms_1.1.0
[26] evaluate_0.14 promises_1.2.0.1 fansi_0.5.0 progress_1.2.2 MAFDash_0.1.0
[31] caTools_1.18.2 DBI_1.1.1 htmlwidgets_1.5.3 stats4_4.0.3 purrr_0.3.4
[36] hash_2.2.6.1 ellipsis_0.3.2 corrplot_0.90 crosstalk_1.1.1.9000 backports_1.2.1
[41] V8_3.4.2 annotate_1.68.0 gridBase_0.4-7 biomaRt_2.46.3 MatrixGenerics_1.2.1
[46] vctrs_0.3.8 Biobase_2.50.0 Cairo_1.5-12.2 withr_2.4.2 cachem_1.0.5
[51] treemap_2.4-2 checkmate_2.0.0 prettyunits_1.1.1 MultiAssayExperiment_1.16.0 cluster_2.1.2
[56] lazyeval_0.2.2 crayon_1.4.1 basilisk.utils_1.2.2 flexdashboard_0.5.2 genefilter_1.72.1
[61] edgeR_3.32.1 labeling_0.4.2 slam_0.1-48 pkgconfig_2.0.3 tweenr_1.0.2
[66] GenomeInfoDb_1.26.7 wordcloud_2.6 vipor_0.4.5 nnet_7.3-16 rlang_0.4.11
[71] lifecycle_1.0.0 downloader_0.4 filelock_1.0.2 tcltk_4.0.3 polyclip_1.10-0
[76] matrixStats_0.60.0 graph_1.68.0 Matrix_1.3-4 Rhdf5lib_1.12.1 base64enc_0.1-3
[81] beeswarm_0.4.0 GlobalOptions_0.1.2 pheatmap_1.0.12 png_0.1-7 viridisLite_0.4.0
[86] rjson_0.2.20 bitops_1.0-7 R.oo_1.24.0 KernSmooth_2.23-20 rhdf5filters_1.2.1
[91] MOFA_1.6.2 blob_1.2.2 TCGAbiolinks_2.18.0 shape_1.4.6 readr_2.0.0
[96] jpeg_0.1-9 S4Vectors_0.28.1 scales_1.1.1 memoise_2.0.0 graphite_1.36.0
[101] GSEABase_1.52.1 magrittr_2.0.1 plyr_1.8.6 gplots_3.1.1 zlibbioc_1.36.0
[106] compiler_4.0.3 mogsa_1.24.0 plotrix_3.8-1 clue_0.3-59 cli_3.0.1
[111] XVector_0.30.0 htmlTable_2.2.1 Formula_1.2-4 MASS_7.3-54 tidyselect_1.1.1
[116] stringi_1.7.3 forcats_0.5.1 TCGAbiolinksGUI.data_1.10.0 textshaping_0.3.5 yaml_2.2.1
[121] GOSemSim_2.16.1 locfit_1.5-9.4 askpass_1.1 latticeExtra_0.6-29 ggrepel_0.9.1
[126] tools_4.0.3 rstudioapi_0.13 canvasXpress_1.35.0 foreach_1.5.1 foreign_0.8-81
[131] gridExtra_2.3 farver_2.1.0 Rtsne_0.15 digest_0.6.27 BiocManager_1.30.16
[136] shiny_1.6.0 proto_1.0.0 Rcpp_1.0.7 GenomicRanges_1.42.0 MOFA2_1.0.1
[141] BiocVersion_3.12.0 later_1.2.0 httr_1.4.2 AnnotationDbi_1.52.0 colorspace_2.0-2
[146] rvest_1.0.1 XML_3.99-0.6 reticulate_1.20 IRanges_2.24.1 splines_4.0.3
[151] uwot_0.1.10 basilisk_1.2.1 systemfonts_1.0.2 plotly_4.9.4.1 xtable_1.8-4
[156] jsonlite_1.7.2 corpcor_1.6.9 NLP_0.2-1 R6_2.5.0 tm_0.7-8
[161] Hmisc_4.5-0 gsubfn_0.7 pillar_1.6.2 htmltools_0.5.1.1 mime_0.11
[166] glue_1.4.2 fastmap_1.1.0 DT_0.18 interactiveDisplayBase_1.28.0 codetools_0.2-18
[171] utf8_1.2.2 lattice_0.20-44 ensurer_1.1 tibble_3.1.3 sqldf_0.4-11
[176] curl_4.3.2 bsplus_0.1.2 svd_0.5 ggbeeswarm_0.6.0 gtools_3.9.2
[181] zip_2.2.0 GO.db_3.12.1 openssl_1.4.4 limma_3.46.0 survival_3.2-11
[186] rmarkdown_2.9 munsell_0.5.0 GetoptLong_1.0.5 rhdf5_2.34.0 GenomeInfoDbData_1.2.4
[191] iterators_1.0.13 HDF5Array_1.18.1 impute_1.64.0 reshape2_1.4.4 gtable_0.3.0
You can set
simple_anno_size = unit(8, "mm")
. If you set argumentannotation_height
, it should look like:annotation_height = unit(c(8,8,8,8,8,8), "mm")
.