xPierKEGG | R Documentation

## Function to visualise prioritised genes in terms of a KEGG pathway

### Description

`xPierKEGG` is supposed to visualise prioritised genes in terms of a KEGG pathway. It returns an object of class "igraph".

### Usage

    xPierKEGG(xTarget, vis = c("net", "evidence", "pathview"), hsa =
    "hsa04621",
    priority.top = NULL, incoming.neighbor.order = 1, nodes_query = NULL,
    largest.comp = TRUE, pathview.filename = NULL,
    pathview.filetype = c("png", "pdf"), verbose = TRUE,
    RData.location = "http://galahad.well.ox.ac.uk/bigdata", ...)

### Arguments

`xTarget` | an object of class "dTarget" or "sTarget"
`vis` | the type of visualisation for a KEGG pathway. It can be one of "net" (visualising the network with nodes colored by priority score; by default), "evidence" for visualising the network with nodes as pie charts, and "pathview" for using the package "pathview"
`hsa` | the identity of KEGG pathway in query. The full list of pathways in human can be found at http://www.genome.jp/kegg-bin/show_organism?menu_type=pathway_maps&org=hsa. For example, 'hsa04621' for 'NOD-like receptor signaling pathway', where the prefix 'hsa' can be ignored
`priority.top` | the number of the top targets. By default, it is NULL meaning no such restriction
`incoming.neighbor.order` | an integer giving the order of the incoming neighborhood. By default, it is 1-order incoming neighborhood
`nodes_query` | which gene in query will be visualised. It (if not null) has the high priority over nodes selected by 'priority.top' and 'incoming.neighbor.order' above
`largest.comp` | logical to indicate whether the largest component is only retained. By default, it sets to true for the largest component being left
`pathview.filename` | the file name saved using the package "pathview". By default, it is NULL meaning "hsa.Pi"
`pathview.filetype` | the file format saved using the package "pathview". It can be "png" or "pdf"
`verbose` | logical to indicate whether the messages will be displayed in the screen. By default, it sets to true
`RData.location` | the characters to tell the location of built-in RData files. See `xRDataLoader` for details
`...` | additional graphic parameters. If the type of visualisation is 'net', see `xVisNet`; if the visualisation type is 'evidence', see `xVisEvidence`

### Value

a subgraph, an object of class "igraph".

### Note

If vis is 'pathview', it will depend on whether a package "pathview" has been installed. It can be installed via: `source("http://bioconductor.org/biocLite.R"); biocLite("pathview")`.

### See Also

`xVisNet`, `xVisEvidence`

### Examples

    ## Not run:
    # Load the library
    library(Pi)

    ## End(Not run)
    RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev"
    ## Not run:
    ## evidence
    xPierKEGG(xTarget, hsa="hsa04621", vis="evidence",
    RData.location=RData.location)
    ## network
    xPierKEGG(xTarget, hsa="hsa04621", vis="net",
    RData.location=RData.location)
    ## using pathview
    pv.out <- xPierKEGG(xTarget, hsa="hsa04621", vis="pathview",
    pathview.filetype=c("png","pdf")[2], RData.location=RData.location)

    ## End(Not run)