Question: topGO: how to print GO descriptions only when using showSigOfNodes?
0
gravatar for anton.kratz
8 months ago by
anton.kratz50
United States, San Diego, UCSD
anton.kratz50 wrote:

I am using topGo following this outline https://datacatz.wordpress.com/2018/01/19/gene-set-enrichment-analysis-with-topgo-part-1/

At the end of my analysis, I visualize the result with showSigOfNodes:

showSigOfNodes(GOdata, score(weight_fisher_result), useInfo = "all", sigForAll=FALSE, firstSigNodes=2,.NO.CHAR=50)

This gives me GO-IDs in each node like this, GO:0008150, which is not very useful to me, I want human-readable text instead. I figured out that another valid value for useInfo is "all", which gives me node labels like this:

GO:0008150
biological_process
1.000000
162 / 13984

  • How can I make it so that the node label is the human-readable description only? I.e. in the example the string "biological_process" only should appear as the node label?
  • What are the valid values for useInfo and how am I supposed to find out what they are? In theĀ showSigOfNodes documentation I only find useInfo: aditional info to be ploted to each node.

> sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] Rgraphviz_2.24.0     biomaRt_2.36.1       topGO_2.32.0        
 [4] SparseM_1.77         GO.db_3.6.0          AnnotationDbi_1.42.1
 [7] IRanges_2.14.10      S4Vectors_0.18.3     Biobase_2.40.0      
[10] graph_1.58.0         BiocGenerics_0.26.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18       compiler_3.5.1     prettyunits_1.0.2  bitops_1.0-6      
 [5] tools_3.5.1        progress_1.2.0     digest_0.6.15      bit_1.1-14        
 [9] RSQLite_2.1.1      memoise_1.1.0      lattice_0.20-35    pkgconfig_2.0.1   
[13] rlang_0.2.2        DBI_1.0.0          rstudioapi_0.7     curl_3.2          
[17] yaml_2.2.0         stringr_1.3.1      httr_1.3.1         hms_0.4.2         
[21] bit64_0.9-7        R6_2.2.2           XML_3.98-1.16      blob_1.1.1        
[25] magrittr_1.5       matrixStats_0.54.0 assertthat_0.2.0   stringi_1.2.4     
[29] RCurl_1.95-4.11    crayon_1.3.4
topgo • 147 views
ADD COMMENTlink written 8 months ago by anton.kratz50
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