Odd Pictures by plotVenn()
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0
Entering edit mode
N. F. • 0
@n-f-8913
Last seen 8.4 years ago
Germany

Hello folks,

I tried to use plotVenn() from the DiffBind-package to compare the differential bound sites generated by DESeq, DESeq2 and edgeR. It seems to work - kinda - but anyhow the output-image looks odd (the circles are not overlapping the right way). Here's a picture of how it looks like:


 

I used the following commands:

db_pliv = dba(sampleSheet = file.path(dataDirectory, 'pliv_chipseq5.csv'))

db_pliv = dba.count(db_pliv, minOverlap = 3)

db_pliv = dba.contrast(db_pliv, minMembers = 2, categories = DBA_TREATMENT)

db_pliv = dba.analyze(db_pliv, method=DBA_ALL_METHODS)

pliv_DB = dba.report(db_pliv, method=DBA_ALL_METHODS, bDB = TRUE, bAll = TRUE)

dba.plotVenn(pliv_DB,1:3,label1="edgeR",label2="DESeq",label3="DESeq2",
             method = DBA_ALL_METHODS, labelAttributes = DBA_ID)

 

Here's my sessioninfo():

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Arch Linux

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8      
[4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8  
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C             
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods 
[10] base     

other attached packages:
[1] DiffBind_1.14.6                        locfit_1.5-9.1                       
[3] biomaRt_2.24.1                         DESeq2_1.8.1                         
[5] RcppArmadillo_0.5.600.2.0              Rcpp_0.12.1                          
[7] limma_3.24.15                          org.Hs.eg.db_3.1.2                   
[9] ggplot2_1.0.1                          PoiClaClu_1.0.2                      
[11] RColorBrewer_1.1-2                     pheatmap_1.0.7                       
[13] GenomicFeatures_1.20.5                 AnnotationDbi_1.30.1                 
[15] Biobase_2.28.0                         airway_0.102.0                       
[17] Gviz_1.12.1                            BSgenome.Plividus.UPalermo.parLiv1_1.0
[19] chipseq_1.18.0                         ShortRead_1.26.0                     
[21] GenomicAlignments_1.4.1                Rsamtools_1.20.4                     
[23] BiocParallel_1.2.22                    BSgenome_1.36.3                      
[25] Biostrings_2.36.4                      XVector_0.8.0                        
[27] rtracklayer_1.28.10                    GenomicRanges_1.20.8                 
[29] GenomeInfoDb_1.4.3                     IRanges_2.2.8                        
[31] S4Vectors_0.6.6                        BiocGenerics_0.14.0                  
[33] RSQLite_1.0.0                          DBI_0.3.1                             

loaded via a namespace (and not attached):
[1] Category_2.34.2           bitops_1.0-6              matrixStats_0.14.2      
[4] tools_3.2.1               rpart_4.1-10              KernSmooth_2.23-15      
[7] Hmisc_3.17-0              colorspace_1.2-6          nnet_7.3-11             
[10] gridExtra_2.0.0           sendmailR_1.2-1           graph_1.46.0            
[13] checkmate_1.6.2           caTools_1.17.1            scales_0.3.0            
[16] BatchJobs_1.6             genefilter_1.50.0         RBGL_1.44.0             
[19] DESeq_1.20.0              stringr_1.0.0             digest_0.6.8            
[22] foreign_0.8-66            AnnotationForge_1.10.1    base64enc_0.1-3         
[25] dichromat_2.0-0           BBmisc_1.9                GOstats_2.34.0          
[28] hwriter_1.3.2             gtools_3.5.0              acepack_1.3-3.3         
[31] VariantAnnotation_1.14.13 RCurl_1.95-4.7            magrittr_1.5            
[34] GO.db_3.1.2               Formula_1.2-1             futile.logger_1.4.1     
[37] Matrix_1.2-2              munsell_0.4.2             proto_0.3-10            
[40] stringi_0.5-5             edgeR_3.10.3              MASS_7.3-44             
[43] zlibbioc_1.14.0           fail_1.3                  gplots_2.17.0           
[46] plyr_1.8.3                gdata_2.17.0              lattice_0.20-33         
[49] splines_3.2.1             annotate_1.46.1           rjson_0.2.15            
[52] systemPipeR_1.2.23        geneplotter_1.46.0        reshape2_1.4.1          
[55] futile.options_1.0.0      XML_3.98-1.3              biovizBase_1.16.0       
[58] latticeExtra_0.6-26       lambda.r_1.1.7            gtable_0.1.2            
[61] amap_0.8-14               xtable_1.7-4              survival_2.38-3         
[64] cluster_2.0.3             brew_1.0-6                GSEABase_1.30.2 

 

Any suggestions what's the problem?

 

plotvenn • 1.1k views
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2
Entering edit mode
Rory Stark ★ 5.1k
@rory-stark-5741
Last seen 9 weeks ago
Cambridge, UK

As you've figured out, DiffBind uses the the vennPlot() function from systemPipeR. It seems to not like certain window sizes/proportions.

Are you plotting to a file or to a graphics window? Try re-sizing (bigger probably) to get the circles to line up with the numbers...

-R

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Thanks for your answer: I am working with RStudio at the moment. When exporting it with larger scale there's nearly no difference except for larger circles.

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Entering edit mode

A limitation of these plots is that they expect a nearly square shaped plotting window. If you reshape your plotting window in Rstudio accordingly then it will work as expected. When you export to file, then you want to use similar plotting dimensions like in the following example (7x7):  

library(systemPipeR)
setlist <- list(A=sample(letters, 18), B=sample(letters, 16), C=sample(letters, 20), D=sample(letters, 22))
vennset <- overLapper(setlist[1:3], type="vennsets")
pdf("venn.pdf", width=7, height=7)
vennPlot(vennset)
dev.off()

 
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Entering edit mode

Thanks for the answer and sorry for the late reply: It's really just a problem with the scale. I tried some rescaling and got different results (some of them look - kinda - good). I'll just look for a proper setting and work with that.

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