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?

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