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fawazfebin
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@fawazfebin-14053
Last seen 4.7 years ago
Hi
I was trying to visualise the bar plot for enrichment analysis using following command in TCGAbiolinks but arrived at " null device" .
> TCGAvisualize_EAbarplot(tf = rownames(ansEA$ResBP),
+ GOBPTab = ansEA$ResBP,
+ GOCCTab = ansEA$ResCC,
+ GOMFTab = ansEA$ResMF,
+ PathTab = ansEA$ResPat,
+ nRGTab = rownames(dataDEGs),
+ nBar = 20)
null device
1
Here is my sessionInfo():
> sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7600) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods [9] base other attached packages: [1] SummarizedExperiment_1.6.5 TCGAbiolinks_2.7.11 DelayedArray_0.2.7 [4] matrixStats_0.52.2 Biobase_2.36.2 GenomicRanges_1.28.6 [7] GenomeInfoDb_1.12.3 IRanges_2.10.5 S4Vectors_0.14.7 [10] BiocGenerics_0.22.1 ggplot2_2.2.1 edgeR_3.18.1 [13] limma_3.32.8 loaded via a namespace (and not attached): [1] colorspace_1.3-2 selectr_0.3-1 [3] rjson_0.2.15 hwriter_1.3.2 [5] class_7.3-14 modeltools_0.2-21 [7] mclust_5.4 circlize_0.4.3 [9] XVector_0.16.0 GlobalOptions_0.0.12 [11] ggpubr_0.1.6 matlab_1.0.2 [13] ggrepel_0.7.0 flexmix_2.3-14 [15] bit64_0.9-7 AnnotationDbi_1.38.2 [17] mvtnorm_1.0-6 xml2_1.1.1 [19] codetools_0.2-15 splines_3.4.2 [21] R.methodsS3_1.7.1 mnormt_1.5-5 [23] doParallel_1.0.11 DESeq_1.28.0 [25] robustbase_0.92-8 geneplotter_1.54.0 [27] knitr_1.18 jsonlite_1.5 [29] Rsamtools_1.28.0 km.ci_0.5-2 [31] broom_0.4.3 annotate_1.54.0 [33] cluster_2.0.6 kernlab_0.9-25 [35] R.oo_1.21.0 readr_1.1.1 [37] compiler_3.4.2 httr_1.3.1 [39] assertthat_0.2.0 Matrix_1.2-12 [41] lazyeval_0.2.1 tools_3.4.2 [43] bindrcpp_0.2 gtable_0.2.0 [45] glue_1.2.0 GenomeInfoDbData_0.99.0 [47] reshape2_1.4.3 dplyr_0.7.4 [49] ggthemes_3.4.0 ShortRead_1.34.2 [51] Rcpp_0.12.14 trimcluster_0.1-2 [53] Biostrings_2.44.2 nlme_3.1-131 [55] rtracklayer_1.36.6 iterators_1.0.9 [57] fpc_2.1-10 psych_1.7.8 [59] stringr_1.2.0 rvest_0.3.2 [61] XML_3.98-1.9 dendextend_1.6.0 [63] DEoptimR_1.0-8 zoo_1.8-0 [65] zlibbioc_1.22.0 MASS_7.3-48 [67] scales_0.5.0 aroma.light_3.6.0 [69] hms_0.4.0 RColorBrewer_1.1-2 [71] curl_3.1 ComplexHeatmap_1.14.0 [73] memoise_1.1.0 gridExtra_2.3 [75] KMsurv_0.1-5 downloader_0.4 [77] biomaRt_2.32.1 latticeExtra_0.6-28 [79] stringi_1.1.6 RSQLite_2.0 [81] genefilter_1.58.1 foreach_1.4.4 [83] GenomicFeatures_1.28.5 BiocParallel_1.10.1 [85] shape_1.4.3 rlang_0.1.6 [87] pkgconfig_2.0.1 prabclus_2.2-6 [89] bitops_1.0-6 lattice_0.20-35 [91] purrr_0.2.4 bindr_0.1 [93] cmprsk_2.2-7 GenomicAlignments_1.12.2 [95] bit_1.1-12 plyr_1.8.4 [97] magrittr_1.5 R6_2.2.2 [99] DBI_0.7 mgcv_1.8-22 [101] foreign_0.8-69 pillar_1.0.1 [103] whisker_0.3-2 survival_2.41-3 [105] RCurl_1.95-4.9 nnet_7.3-12 [107] tibble_1.4.1 EDASeq_2.10.0 [109] survMisc_0.5.4 viridis_0.4.0 [111] GetoptLong_0.1.6 locfit_1.5-9.1 [113] grid_3.4.2 sva_3.24.4 [115] data.table_1.10.4-3 blob_1.1.0 [117] ConsensusClusterPlus_1.40.0 digest_0.6.13 [119] diptest_0.75-7 xtable_1.8-2 [121] tidyr_0.7.2 R.utils_2.6.0 [123] munsell_0.4.3 viridisLite_0.2.0 [125] survminer_0.4.1
Can anyone help please ? Thanks in advance.