arrangePathview {MAGeCKFlute}R Documentation

Kegg pathway view and arrange grobs on page

Description

Kegg pathway view and arrange grobs on page.

Usage

arrangePathview(genelist, pathways = c(), top = 4, ncol = 2,
  title = "Group A", sub = "Negative control normalized",
  organism = "hsa", view_allpath = FALSE, output = ".",
  path.archive = ".", kegg.native = TRUE)

Arguments

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).

view_allpath

boolean, specifying whether view all pathways. Default view_allpath='FALSE', and only plot top enriched pathways.

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.

Value

plot on the current device

Author(s)

Wubing Zhang

See Also

KeggPathwayView

Examples

data(mle.gene_summary)
# Read beta score from gene summary table in MAGeCK MLE results
dd = ReadBeta(mle.gene_summary)
colnames(dd)[2:3] = c("Control", "Treatment")
arrangePathview(dd, "hsa00534", title=NULL, sub=NULL, organism="hsa")


[Package MAGeCKFlute version 1.4.3 Index]