Question: TCGAvisualize_EAbarplot error in TCGAbiolinks
0
gravatar for fawazfebin
21 months ago by
fawazfebin30
fawazfebin30 wrote:

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.

 

ADD COMMENTlink written 21 months ago by fawazfebin30
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