xPierKEGG | R Documentation |
xPierKEGG
is supposed to visualise prioritised genes in terms of
a KEGG pathway. It returns an object of class "igraph".
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", ...)
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 |
... |
additional graphic parameters. If the type of visualisation
is 'net', see |
a subgraph, an object of class "igraph".
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")
.
xVisNet
, xVisEvidence
## 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)