phyloseq heatmap blank after multiple package updates
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newmanss • 0
Last seen 4.6 years ago
United States


After updating multiple packages, my phyloseq heatmaps are blank.  I have tried running previously run analyses that worked and running using older package versions but I have been unable to isolate the problem.  The heatmap is drawn and it is labeled correctly but the heatmap itself is gray with a white grid. Can someone please help me fix this?

hmOrder <- plot_heatmap(phyOrder, taxa.label = "Order", sample.order = "expvar")
hmOrder + ggtitle("Heatmap by Order") + theme(axis.text = element_text(size = 8), 
    axis.title = element_text(size = 14, face = "bold"))


Warning:  Transformation introduced infinite values in discrete y-axis


R version 3.4.1 (2017-06-30)
  Platform: x86_64-w64-mingw32/x64 (64-bit)
  Running under: Windows 7 x64 (build 7601) Service Pack 1
  Matrix products: default
  [1] LC_COLLATE=English_United States.1252 
  [2] LC_CTYPE=English_United States.1252   
  [3] LC_MONETARY=English_United States.1252
  [4] LC_NUMERIC=C                          
  [5] LC_TIME=English_United States.1252    
  attached base packages:
   [1] stats4    parallel  grid      stats     graphics  grDevices utils    
   [8] datasets  methods   base     
  other attached packages:
   [1] gtools_3.5.0               biom_0.3.12               
   [3] DESeq2_1.12.2              SummarizedExperiment_1.2.2
   [5] Biobase_2.32.0             GenomicRanges_1.24.2      
   [7] GenomeInfoDb_1.8.2         IRanges_2.6.0             
   [9] S4Vectors_0.10.1           BiocGenerics_0.18.0       
  [11] vegan_2.4-4                lattice_0.20-35           
  [13] permute_0.9-4              tidyr_0.7.0               
  [15] doParallel_1.0.10          iterators_1.0.8           
  [17] foreach_1.4.3              dplyr_0.7.2               
  [19] plyr_1.8.4                 scales_0.5.0              
  [21] ggplot2_2.2.1              ape_4.1                   
  [23] phyloseq_1.14.0            shiny_1.0.5               
  loaded via a namespace (and not attached):
   [1] nlme_3.1-131         bit64_0.9-7          RColorBrewer_1.1-2  
   [4] rprojroot_1.2        tools_3.4.1          backports_1.1.0     
   [7] R6_2.2.2             rpart_4.1-11         Hmisc_4.0-3         
  [10] DBI_0.7              lazyeval_0.2.0       mgcv_1.8-17         
  [13] colorspace_1.3-2     ade4_1.7-8           nnet_7.3-12         
  [16] gridExtra_2.2.1      bit_1.1-12           compiler_3.4.1      
  [19] formatR_1.5          htmlTable_1.9        checkmate_1.8.3     
  [22] genefilter_1.54.2    stringr_1.2.0        digest_0.6.12       
  [25] foreign_0.8-69       rmarkdown_1.6        XVector_0.12.0      
  [28] base64enc_0.1-3      pkgconfig_2.0.1      htmltools_0.3.6     
  [31] htmlwidgets_0.9      rlang_0.1.2          RSQLite_2.0         
  [34] bindr_0.1            jsonlite_1.5         BiocParallel_1.6.2  
  [37] acepack_1.4.1        magrittr_1.5         Formula_1.2-2       
  [40] Matrix_1.2-10        Rcpp_0.12.12         munsell_0.4.3       
  [43] stringi_1.1.5        yaml_2.1.14          MASS_7.3-47         
  [46] RJSONIO_1.3-0        zlibbioc_1.18.0      blob_1.1.0          
  [49] Biostrings_2.40.1    splines_3.4.1        multtest_2.28.0     
  [52] annotate_1.50.0      locfit_1.5-9.1       knitr_1.17          
  [55] igraph_1.1.2         geneplotter_1.50.0   reshape2_1.4.2      
  [58] codetools_0.2-15     XML_3.98-1.9         glue_1.1.1          
  [61] evaluate_0.10.1      latticeExtra_0.6-28  data.table_1.10.4   
  [64] httpuv_1.3.5         gtable_0.2.0         purrr_0.2.3         
  [67] assertthat_0.2.0     mime_0.5             xtable_1.8-2        
  [70] survival_2.41-3      tibble_1.3.4         memoise_1.1.0       
  [73] AnnotationDbi_1.34.3 bindrcpp_0.2         cluster_2.0.6
phyloseq heatmap • 779 views
Entering edit mode
Last seen 1 day ago
EMBL European Molecular Biology Laborat…

Can you post a minimal working example (with all the code) to reproduce your problem, also the input data (can be "made up") and an example output file (.png, .pdf)? This is most likely the precondition for a specific and helpful reply..


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