I’m finding your ChipSeeker very very useful, but I have a question. When I use plotAveProf2 with facets turned on, the order of the panels is not what I’d like - I’d like them to be in the order of the bed file list I created. Is there a way to enforce that order, or to specify a particular order? I haven't been able to find how to do this from the on-line vignette or R help page for the function. Here's the command I’m using:
plotAvgProf2(sets, TxDb=txdb, upstream=2500, downstream=2500, xlab="Genomic Region (5'->3')", ylab = "Read Count Frequency", conf=0.95,resample=100, facet="row", free_y = FALSE)
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)
locale:
[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] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] clusterProfiler_3.0.5 DOSE_2.10.7
[3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.24.5
[5] AnnotationDbi_1.34.4 Biobase_2.32.0
[7] GenomicRanges_1.24.3 GenomeInfoDb_1.8.7
[9] IRanges_2.6.1 S4Vectors_0.10.3
[11] BiocGenerics_0.18.0 ChIPseeker_1.8.9
loaded via a namespace (and not attached):
[1] Rcpp_0.12.7 lattice_0.20-34 GO.db_3.3.0
[4] tidyr_0.6.0 Rsamtools_1.24.0 Biostrings_2.40.2
[7] gtools_3.5.0 assertthat_0.1 gridBase_0.4-7
[10] R6_2.1.3 plyr_1.8.4 RSQLite_1.0.0
[13] ggplot2_2.1.0 gplots_3.0.1 zlibbioc_1.18.0
[16] annotate_1.50.0 gdata_2.17.0 SparseM_1.72
[19] qvalue_2.4.2 splines_3.3.1 BiocParallel_1.6.6
[22] stringr_1.1.0 topGO_2.24.0 igraph_1.0.1
[25] RCurl_1.95-4.8 biomaRt_2.28.0 munsell_0.4.3
[28] rtracklayer_1.32.2 SummarizedExperiment_1.2.3 tibble_1.2
[31] gridExtra_2.2.1 matrixStats_0.50.2 XML_3.98-1.4
[34] dplyr_0.5.0 GenomicAlignments_1.8.4 bitops_1.0-6
[37] grid_3.3.1 xtable_1.8-2 GSEABase_1.34.1
[40] gtable_0.2.0 DBI_0.5-1 magrittr_1.5
[43] scales_0.4.0 graph_1.50.0 KernSmooth_2.23-15
[46] stringi_1.1.1 GOSemSim_1.30.3 XVector_0.12.1
[49] reshape2_1.4.1 DO.db_2.9 boot_1.3-18
[52] RColorBrewer_1.1-2 tools_3.3.1 plotrix_3.6-3
[55] colorspace_1.2-6 UpSetR_1.2.4 caTools_1.17.1
Miles A. Pufall
University of Iowa
