arrangePathview: Kegg pathway view and arrange grobs on page

In WubingZhang/MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

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 = NULL,
  sub = NULL,
  organism = "hsa",
  output = ".",
  path.archive = ".",
  kegg.native = TRUE,
  verbose = 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).
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

Value

plot on the current device

Author(s)

Wubing Zhang

Examples

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")

WubingZhang/MAGeCKFlute documentation built on Jan. 27, 2024, 2:43 p.m.