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anton.kratz
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@antonkratz-8836
Last seen 7 months ago
Japan, Tokyo, The Systems Biology Insti…
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 the 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