arrangePathview {MAGeCKFlute} | R Documentation |
Kegg pathway view and arrange grobs on page.
arrangePathview( genelist, pathways = c(), top = 4, ncol = 2, title = NULL, sub = NULL, organism = "hsa", output = ".", path.archive = ".", kegg.native = TRUE, verbose = TRUE )
genelist |
a data frame with columns of ENTREZID, Control and Treatment. The columns of Control and Treatment represent gene score in Control and Treatment sample. |
pathways |
character vector, the KEGG pathway ID(s), usually 5 digit, may also include the 3 letter KEGG species code. |
top |
integer, specifying how many top enriched pathways to be visualized. |
ncol |
integer, specifying how many column of figures to be arranged in each page. |
title |
optional string, or grob. |
sub |
optional string, or grob. |
organism |
character, either the kegg code, scientific name or the common name of the target species. This applies to both pathway and gene.data or cpd.data. When KEGG ortholog pathway is considered, species="ko". Default species="hsa", it is equivalent to use either "Homo sapiens" (scientific name) or "human" (common name). |
output |
Path to save plot to. |
path.archive |
character, the directory of KEGG pathway data file (.xml) and image file (.png). Users may supply their own data files in the same format and naming convention of KEGG's (species code + pathway id, e.g. hsa04110.xml, hsa04110.png etc) in this directory. Default kegg.dir="." (current working directory). |
kegg.native |
logical, whether to render pathway graph as native KEGG graph (.png) or using graphviz layout engine (.pdf). Default kegg.native=TRUE. |
verbose |
Boolean |
plot on the current device
Wubing Zhang
file3 = file.path(system.file("extdata", package = "MAGeCKFlute"), "testdata/mle.gene_summary.txt") dd = ReadBeta(file3) colnames(dd)[2:3] = c("Control", "Treatment") # arrangePathview(dd, c("hsa00534"), title=NULL, sub=NULL, organism="hsa")