I’m using the clusterProfiler to enrich my gene list. However, all the codes can be executed, but not figure can be presented. It looks the plot device has some problem, but I don’t why and how to fix it out. Could you please give me a troubleshooting? Thanks.
The codes are shown below:
list = infRBC_vs_unRBC_R_FC1.2adjP0.2$geneEG
x = groupGO(gene = list, 'lumiHumanAll.db', ont = "MF", level = 2, readable = TRUE)
y = enrichGO(gene = list, 'lumiHumanAll.db' ,ont = "MF", pvalueCutoff = 0.01, readable = TRUE)
z = enrichKEGG(gene = list, organism = "hsa", pvalueCutoff = 0.05)
plot(x)
plot(y)
plot(z)
sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)
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] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] lumiHumanAll.db_1.22.0 org.Hs.eg.db_3.3.0 AnnotationDbi_1.34.4 IRanges_2.6.1
[5] S4Vectors_0.10.2 Biobase_2.32.0 BiocGenerics_0.18.0 limma_3.28.17
[9] clusterProfiler_3.0.4 DOSE_2.10.7
loaded via a namespace (and not attached):
[1] Rcpp_0.12.6 plyr_1.8.4 tools_3.3.1 annotate_1.50.0 RSQLite_1.0.0
[6] tibble_1.1 gtable_0.2.0 lattice_0.20-33 igraph_1.0.1 graph_1.50.0
[11] DBI_0.5 SparseM_1.7 topGO_2.24.0 stringr_1.0.0 grid_3.3.1
[16] qvalue_2.4.2 GSEABase_1.34.0 XML_3.98-1.4 GOSemSim_1.30.3 GO.db_3.3.0
[21] ggplot2_2.1.0 reshape2_1.4.1 DO.db_2.9 tidyr_0.6.0 magrittr_1.5
[26] scales_0.4.0 matrixStats_0.50.2 splines_3.3.1 assertthat_0.1 colorspace_1.2-6
[31] xtable_1.8-2 stringi_1.1.1 munsell_0.4.3
