xPierKEGGR 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: BiocManager::install("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"
## 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)