ComplexHeatmap: Not able to change the annotations size of the heatmap
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Entering edit mode
@ashish-jain-14944
Last seen 7 weeks ago
Iowa State University

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
ComplexHeatmap Anno Annotation • 153 views
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Entering edit mode

You can set simple_anno_size = unit(8, "mm"). If you set argument annotation_height, it should look like: annotation_height = unit(c(8,8,8,8,8,8), "mm").

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