View Single Post
Old 03-20-2014, 04:59 AM   #43
sindrle
Senior Member
 
Location: Norway

Join Date: Aug 2013
Posts: 266
Default

Im having problems with Pathview. I can only get native KEGG, the kegg.native=F does not work.

Also the native KEGG only has green color, not red (up regulated) and green (down regulated).

Why am I having these two problems?

Native KEGG
# pv.out.list <- sapply(path.ids2, function(pid) pathview(gene.data = d[,
# 1:2], pathway.id = pid, species = "hsa", kegg.dir = "~/RNAseq/13_Acute-Changes/13_GAGE_native_A1A2/A1A2pT2D/Pathview"))

Graphviz view
# pv.out.list <- sapply(path.ids2, function(pid) pathview(gene.data = d[,
# 1:2], pathway.id = pid, species = "hsa", kegg.native=F,
# sign.pos="bottomleft", kegg.dir = "~/RNAseq/13_Acute-Changes/13_GAGE_native_A1A2/A1A2pT2D/Pathview"))


# > sessionInfo()
# R version 3.0.3 (2013-09-25)
# Platform: x86_64-apple-darwin10.8.0 (64-bit)

# 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] parallel stats graphics grDevices utils datasets methods
# [8] base

# other attached packages:
# [1] Rsamtools_1.14.3
# [2] Biostrings_2.30.1
# [3] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
# [4] GenomicFeatures_1.14.5
# [5] AnnotationDbi_1.24.0
# [6] Biobase_2.22.0
# [7] GenomicRanges_1.14.4
# [8] XVector_0.2.0
# [9] IRanges_1.20.7
# [10] BiocGenerics_0.8.0
# [11] BiocInstaller_1.12.0

# loaded via a namespace (and not attached):
# [1] biomaRt_2.18.0 bitops_1.0-6 BSgenome_1.30.0
# [4] DBI_0.2-7 RCurl_1.95-4.1 RSQLite_0.11.4
# [7] rtracklayer_1.22.5 stats4_3.0.2 tools_3.0.2
# [10] XML_3.95-0.2 zlibbioc_1.8.0
sindrle is offline   Reply With Quote