Heatmap with foldchange displayed

[suekn]

Using heatmap(), I cannot get the foldChange to display properly. It looks the same as without fold change. I followed tutorial 15.4 and I believe my gene_list is equivalent.

I am using following csv: DESeq2_kallisto_MM003_MM007_MM011_vs_MM027_MM031_MM035-DEG_list.csv

library(clusterProfiler)

organism = "org.Hs.eg.db"
library(organism, character.only = TRUE)

 # in this overrepresentation analysis, we define DEGs as
  # log FC > 2 and padj < 0.05
  
  # reading in input from deseq2
  df = read.csv(as.character(file))
  
  # we want the log2 fold change 
  original_gene_list <- df$log2FoldChange
  
  # name the vector
  names(original_gene_list) <- df$X
  
  # omit any NA values 
  gene_list<-na.omit(original_gene_list)
  
  # sort the list in decreasing order (required for clusterProfiler)
  gene_list = sort(gene_list, decreasing = TRUE)
  
  # Exctract significant results (padj < 0.05)
  sig_genes_df = subset(df, padj < 0.05)
  
  # From significant results, we want to filter on log2fold change
  genes <- sig_genes_df$log2FoldChange
  
  # Name the vector
  names(genes) <- sig_genes_df$X
  
  # omit NA values
  genes <- na.omit(genes)
  
  # filter on min log2fold change (log2FoldChange > 2)
  genes <- names(genes)[abs(genes) > 2]
  
  go_enrich <- enrichGO(gene = genes,
                        universe = names(gene_list),
                        OrgDb = organism, 
                        keyType = 'SYMBOL',
                        readable = T,
                        ont = "BP",
                        pvalueCutoff = 0.05,
                        qvalueCutoff = 0.10,
                        pAdjustMethod = 'none')

library(enrichplot)
  heatplot(go_enrich, showCategory = 5)

  heatplot(go_enrich, foldChange=gene_list, showCategory=5)

[huerqiang]

It works well with me:

[suekn]

In the tutorial, I was wondering if the issue was that it used EntrezIDs whereas I used Symbol. However, my code worked on your computer.

Would you mind showing what you have for:

1. sessionInfo()
2. go_enrich
3. gene_list

[huerqiang]

sessionInfo() R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8 LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C LC_TIME=Chinese (Simplified)_China.utf8

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] enrichplot_1.17.2.991 org.Hs.eg.db_3.15.0 AnnotationDbi_1.58.0 IRanges_2.30.0 S4Vectors_0.34.0 Biobase_2.56.0 BiocGenerics_0.42.0 clusterProfiler_4.5.3

loaded via a namespace (and not attached): [1] ggtree_3.4.2 fgsea_1.22.0 colorspace_2.0-3 gson_0.0.7 ellipsis_0.3.2 qvalue_2.28.0 XVector_0.36.0 fs_1.5.2 aplot_0.1.6 farver_2.1.1
[11] remotes_2.4.2 graphlayouts_0.8.1 ggrepel_0.9.1 bit64_4.0.5 scatterpie_0.1.8 fansi_1.0.3 KEGG.db_1.0 codetools_0.2-18 splines_4.2.1 cachem_1.0.6
[21] GOSemSim_2.22.0 polyclip_1.10-0 pkgload_1.3.0 jsonlite_1.8.0 DOyulab.db_0.1.0 GO.db_3.15.0 png_0.1-7 ggforce_0.3.3 shiny_1.7.2 compiler_4.2.1
[31] httr_1.4.4 lazyeval_0.2.2 assertthat_0.2.1 Matrix_1.4-1 fastmap_1.1.0 cli_3.3.0 later_1.3.0 tweenr_2.0.0 htmltools_0.5.3 prettyunits_1.1.1
[41] tools_4.2.1 igraph_1.3.4 gtable_0.3.0 glue_1.6.2 GenomeInfoDbData_1.2.8 reshape2_1.4.4 dplyr_1.0.9 fastmatch_1.1-3 Rcpp_1.0.8.3 vctrs_0.4.1
[51] Biostrings_2.64.0 nlme_3.1-159 ape_5.6-2 ggraph_2.0.6 stringr_1.4.0 ps_1.7.1 mime_0.12 miniUI_0.1.1.1 lifecycle_1.0.1 devtools_2.4.4
[61] DOSE_3.23.2 zlibbioc_1.42.0 MASS_7.3-58.1 scales_1.2.0 tidygraph_1.2.1 promises_1.2.0.1 parallel_4.2.1 RColorBrewer_1.1-3 curl_4.3.2 memoise_2.0.1
[71] gridExtra_2.3 ggfun_0.0.6 ggplot2_3.3.6 downloader_0.4 yulab.utils_0.0.5 stringi_1.7.6 RSQLite_2.2.14 tidytree_0.4.0 pkgbuild_1.3.1 BiocParallel_1.30.3
[81] GenomeInfoDb_1.32.3 rlang_1.0.4 pkgconfig_2.0.3 bitops_1.0-7 lattice_0.20-45 purrr_0.3.4 labeling_0.4.2 treeio_1.20.2 patchwork_1.1.1 htmlwidgets_1.5.4
[91] shadowtext_0.1.2 bit_4.0.4 processx_3.7.0 tidyselect_1.1.2 plyr_1.8.7 magrittr_2.0.3 R6_2.5.1 generics_0.1.3 profvis_0.3.7 DBI_1.1.3
[101] pillar_1.8.0 withr_2.5.0 KEGGREST_1.36.3 RCurl_1.98-1.7 tibble_3.1.8 crayon_1.5.1 utf8_1.2.2 urlchecker_1.0.1 viridis_0.6.2 usethis_2.1.6
[111] grid_4.2.1 data.table_1.14.2 blob_1.2.3 callr_3.7.1 digest_0.6.29 xtable_1.8-4 tidyr_1.2.0 httpuv_1.6.5 gridGraphics_0.5-1 munsell_0.5.0
[121] ggplotify_0.1.0 viridisLite_0.4.0 sessioninfo_1.2.2

[huerqiang]

This has nothing to do with the version of the software, you should check that you have executed your code correctly.

[suekn]

Thank you! I'm not sure why my code would execute differently. Would you mind showing:

1. go_enrich object
2. gene_list

I just want to make sure our results after running the enrichment anaylsis are truly the same.

[huerqiang]

@suekn Please provide your email.

[suekn]

[email protected]