Question: Downstream proportions are not identical in vennpie and upsetplot results
0
gravatar for afli
3 days ago by
afli0
China, Beijing, IGDB
afli0 wrote:

enter image description here

Hi, I find that the peaks in downstream region is zero in upsetplot, but it take up some part in ven plot. Where is this difference come from? Thank you!

chipseeker upsetplot • 95 views
ADD COMMENTlink modified 2 days ago by dariober9.2k • written 3 days ago by afli0

any reproducible example?

ADD REPLYlink written 2 days ago by Guangchuang Yu1.9k

Yes, I used the example in your tutorial, and the same issue occur. My command lines are as follows:

library(ChIPseeker)

files <- getSampleFiles()

peak <- readPeakFile(files[[4]])

require(TxDb.Hsapiens.UCSC.hg19.knownGene)

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

peakAnno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000),TxDb=txdb)

pdf("upsetplot_test.pdf",width =13, height=7)

upsetplot(peakAnno, vennpie=TRUE)

dev.off()

In the pdf file, downstream region is always False, and be zero.My session information is as follows:

sessionInfo()

R version 3.5.0 (2018-04-23)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 14.04.5 LTS

Matrix products: default

BLAS: /mnt/tiger/afli/softwares/R3.5.0_afli/lib/R/lib/libRblas.so

LAPACK: /mnt/tiger/afli/softwares/R3.5.0_afli/lib/R/lib/libRlapack.so

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [2] GenomicFeatures_1.32.0
[3] AnnotationDbi_1.42.1
[4] Biobase_2.40.0
[5] GenomicRanges_1.32.3
[6] GenomeInfoDb_1.16.0
[7] IRanges_2.14.10
[8] S4Vectors_0.18.3
[9] BiocGenerics_0.26.0
[10] ChIPseeker_1.16.0

loaded via a namespace (and not attached): [1] bitops_1.0-6 matrixStats_0.53.1
[3] enrichplot_1.0.2 bit64_0.9-7
[5] RColorBrewer_1.1-2 progress_1.2.0
[7] httr_1.3.1 UpSetR_1.3.3
[9] tools_3.5.0 R6_2.2.2
[11] KernSmooth_2.23-15 DBI_1.0.0
[13] lazyeval_0.2.1 colorspace_1.3-2
[15] tidyselect_0.2.4 gridExtra_2.3
[17] prettyunits_1.0.2 bit_1.1-14
[19] compiler_3.5.0 DelayedArray_0.6.1
[21] labeling_0.3 rtracklayer_1.40.3
[23] caTools_1.17.1 scales_0.5.0
[25] ggridges_0.5.0 stringr_1.3.1
[27] digest_0.6.15 Rsamtools_1.32.0
[29] DOSE_3.6.1 XVector_0.20.0
[31] pkgconfig_2.0.1 plotrix_3.7-2
[33] rlang_0.2.1 RSQLite_2.1.1
[35] bindr_0.1.1 gtools_3.8.1
[37] BiocParallel_1.14.1 GOSemSim_2.6.0
[39] dplyr_0.7.6 RCurl_1.95-4.10
[41] magrittr_1.5 GO.db_3.6.0
[43] GenomeInfoDbData_1.1.0 Matrix_1.2-14 [45] Rcpp_0.12.17 munsell_0.5.0
[47] viridis_0.5.1 stringi_1.2.3
[49] ggraph_1.0.2 MASS_7.3-50
[51] SummarizedExperiment_1.10.1 zlibbioc_1.26.0
[53] gplots_3.0.1 plyr_1.8.4
[55] qvalue_2.12.0 grid_3.5.0
[57] blob_1.1.1 gdata_2.18.0
[59] ggrepel_0.8.0 DO.db_2.9
[61] crayon_1.3.4 lattice_0.20-35
[63] Biostrings_2.48.0 cowplot_0.9.2
[65] splines_3.5.0 hms_0.4.2
[67] pillar_1.2.3 fgsea_1.6.0
[69] igraph_1.2.1 boot_1.3-20
[71] reshape2_1.4.3 biomaRt_2.36.1
[73] fastmatch_1.1-0 XML_3.98-1.11
[75] glue_1.2.0 data.table_1.11.4
[77] tweenr_0.1.5 gtable_0.2.0
[79] purrr_0.2.5 assertthat_0.2.0
[81] ggplot2_3.0.0 gridBase_0.4-7
[83] ggforce_0.1.3 viridisLite_0.3.0
[85] tibble_1.4.2 GenomicAlignments_1.16.0
[87] memoise_1.1.0 units_0.6-0
[89] bindrcpp_0.2.2

This is my upsetplot pdf file

ADD REPLYlink written 2 days ago by afli0
0
gravatar for dariober
2 days ago by
dariober9.2k
Glasgow - UK
dariober9.2k wrote:

I haven't thought carefully about your question but the first explanation that comes to my mind is that proportional Venn diagrams with 3 or more sets are not always possible. See this post Venn/Euler Diagram Of Four Or More Sets.

ADD COMMENTlink written 2 days ago by dariober9.2k

Thanks my friend, I see the post and UpSetR is recommended in the reply, I do not quite understand it why proportional Venn diagrams with 3 or more sets are not always possible, because UpSetR can easily handle six sets. Maybe I should think your advice further.

ADD REPLYlink written 2 days ago by afli0
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