I'm trying to use Pathview for pathway analysis of my differentially expressed genes. I used the below command
pv.out <- pathview(gene.data =DE, gene.idtype = "kegg", pathway.id = "00480", species = "ath", out.suffix = "DE.glu", kegg.native = T)
While my input file was the combination of up and down regulated genes, indicated by log FC, Pathview returned just up-regulated genes (red color) on the pathway. Please kindly tell me how I should fix this problem to see both, red and green (down-regulated genes), on the pathway?
Here is sessionInfo()
R version 3.3.1 (2016-06-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  parallel stats4 stats graphics grDevices utils datasets  methods base other attached packages:  pathview_1.10.1 org.Hs.eg.db_3.2.3 RSQLite_1.0.0  DBI_0.4-1 AnnotationDbi_1.32.3 IRanges_2.4.8  S4Vectors_0.8.11 Biobase_2.30.0 BiocGenerics_0.16.1 loaded via a namespace (and not attached):  KEGGgraph_1.28.0 XML_3.98-1.4 Biostrings_2.38.4 png_0.1-7  R6_2.1.2 grid_3.3.1 httr_1.2.0 graph_1.48.0  zlibbioc_1.16.0 curl_0.9.7 XVector_0.10.0 Rgraphviz_2.14.0  tools_3.3.1 KEGGREST_1.10.1