Question: viewPathway not showing a gene of interest
gravatar for santos22903
10 weeks ago by
santos229030 wrote:


I was trying to use ReactomePA package to visualize a pathway of interest and a gene of interest. Unfortunately, while the pathway is showing a lot of genes belonging to the pathway, I cannot find mine. I interactively checked it as follows, but the gene is not showing (would be the only one not quasi-grey in this example):

> require(ReactomePA)
> path2vis <- "Platelet activation, signaling and aggregation"
> testVec<-c(-0.81)
> names(testVec)<-c(108101)
> viewPathway(path2vis,organism="mouse",readable=T,foldChange=testVec)
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

[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    
[7] datasets  methods   base     

other attached packages:
 [1]   AnnotationDbi_1.44.0
 [4] IRanges_2.16.0       S4Vectors_0.20.1     Biobase_2.42.0      
 [7] BiocGenerics_0.28.0  graphite_1.28.2      biomaRt_2.38.0      
[10] ReactomePA_1.26.0    openxlsx_4.1.0      

loaded via a namespace (and not attached):
 [1] bitops_1.0-6        enrichplot_1.2.0    bit64_0.9-7        
 [4] RColorBrewer_1.1-2  progress_1.2.0      httr_1.4.0         
 [7] UpSetR_1.3.3        tools_3.5.2         backports_1.1.3    
[10] R6_2.3.0            DBI_1.0.0           lazyeval_0.2.1     
[13] colorspace_1.4-0    tidyselect_0.2.5    gridExtra_2.3      
[16] prettyunits_1.0.2   curl_3.3            bit_1.1-14         
[19] compiler_3.5.2      graph_1.60.0        xml2_1.2.0         
[22] labeling_0.3        triebeard_0.3.0     scales_1.0.0       
[25] checkmate_1.9.1     ggridges_0.5.1      rappdirs_0.3.1     
[28] stringr_1.3.1       digest_0.6.18       DOSE_3.8.2         
[31] pkgconfig_2.0.2     rlang_0.3.1         RSQLite_2.1.1      
[34] bindr_0.1.1         gridGraphics_0.3-0  farver_1.1.0       
[37] jsonlite_1.6        BiocParallel_1.16.5 GOSemSim_2.8.0     
[40] dplyr_0.7.8         zip_1.0.0           RCurl_1.95-4.11    
[43] magrittr_1.5        ggplotify_0.0.3     GO.db_3.7.0        
[46] Matrix_1.2-15       Rcpp_1.0.0          munsell_0.5.0      
[49] viridis_0.5.1       stringi_1.2.4       ggraph_1.0.2       
[52] MASS_7.3-51.1       plyr_1.8.4          qvalue_2.14.1      
[55] grid_3.5.2          blob_1.1.1          ggrepel_0.8.0      
[58] DO.db_2.9           crayon_1.3.4        lattice_0.20-38    
[61] cowplot_0.9.4       splines_3.5.2       hms_0.4.2          
[64] pillar_1.3.1        fgsea_1.8.0         igraph_1.2.2       
[67] reshape2_1.4.3      fastmatch_1.1-0     XML_3.98-1.16      
[70] glue_1.3.0          data.table_1.12.0   tweenr_1.0.1       
[73] urltools_1.7.1      gtable_0.2.0        purrr_0.3.0        
[76] assertthat_0.2.0    ggplot2_3.1.0       ggforce_0.1.3      
[79] europepmc_0.3       reactome.db_1.66.0  viridisLite_0.3.0  
[82] tibble_2.0.1        rvcheck_0.1.3       memoise_1.1.0      
[85] units_0.6-2         bindrcpp_0.2.2 

So, when I run this, I do not get any changed genes in the pathway shown, whereas Fermt3 (entrezID 108101) should definitely be there. Could you, please, tell me what the problem might be. Thank you

reactomepa • 108 views
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