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, organism="hsa")
    colnames(dd)[3:4] = c("Control", "Treatment")
    arrangePathview(dd, "hsa00534", title=NULL, sub=NULL, organism="hsa")

[Package MAGeCKFlute version 1.2.3 Index]