xVisEvidence: Function to visualise evidence for prioritised genes in a...

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Description

xVisEvidence is supposed to visualise evidence for prioritised genes in a gene network. It returns an object of class "igraph".

Usage

xVisEvidence(
xTarget,
g = NA,
nodes = NULL,
node.info = c("smart", "none"),
neighbor.order = 1,
neighbor.seed = TRUE,
neighbor.top = NULL,
largest.comp = TRUE,
show = TRUE,
colormap = "ggplot2",
legend.position = "topleft",
legend.horiz = FALSE,
mtext.side = 3,
verbose = TRUE,
edge.width = NULL,
vertex.size = NULL,
vertex.size.nonseed = NULL,
vertex.label.color = "blue",
vertex.label.color.nonseed = NULL,
...
)

Arguments

xTarget	an object of class "dTarget", "sTarget" or "eTarget"
g	an object of class "igraph". If NA, the 'metag' will be used, which is part of the input object "xTarget". If provided, it must have a node attribute called 'priority'
nodes	which node genes are in query. If NULL, the top gene will be queried
node.info	tells the additional information used to label nodes. It can be one of "none" (only gene labeling), "smart" for (by default) using three pieces of information (if any): genes, 5-star ratings, and associated ranks (marked by an @ icon)
neighbor.order	an integer giving the order of the neighborhood. By default, it is 1-order neighborhood
neighbor.seed	logical to indicate whether neighbors are seeds only. By default, it sets to true
neighbor.top	the top number of the neighbors with the highest priority. By default, it sets to NULL to disable this parameter
largest.comp	logical to indicate whether the largest component is only retained. By default, it sets to true for the largest component being left
show	logical to indicate whether to show the graph
colormap	short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta), and "ggplot2" (emulating ggplot2 default color palette). Alternatively, any hyphen-separated HTML color names, e.g. "lightyellow-orange" (by default), "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names
legend.position	the legend position. If NA, the legend is not shown
legend.horiz	logical specifying the legend horizon. If TRUE, set the legend horizontally rather than vertically
mtext.side	the side of marginal text. If NA, it is not shown
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display
edge.width	the width of the edge. If NULL, the width edge is proportional to the 'weight' edge attribute (if existed)
vertex.size	the size of each vertex. If null, each vertex has the size proportional to the degree of nodes
vertex.size.nonseed	the size of each nonseed vertex. If null, each vertex has the size proportional to the degree of nodes
vertex.label.color	the color of vertex labels
vertex.label.color.nonseed	the color of nonseed vertex labels
...	additional graphic parameters. See http://igraph.org/r/doc/plot.common.html for the complete list.

Value

a subgraph, an object of class "igraph".

See Also

xColormap

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
## TNFRSF1A
xVisEvidence(xTarget, nodes="TNFRSF1A", neighbor.order=1,
neighbor.seed=TRUE, neighbor.top=NULL, vertex.label.color="black",
vertex.label.cex=0.7, vertex.label.dist=0.6, vertex.label.font=1,
vertex.label.family="Arial", legend.position="bottomleft",
legend.horiz=TRUE, newpage=FALSE)
## UBA52
xVisEvidence(xTarget, nodes="UBA52", neighbor.order=1,
neighbor.seed=TRUE, neighbor.top=20, vertex.label.color="black",
vertex.label.cex=0.7, vertex.label.dist=0.6, vertex.label.font=1,
legend.position="bottomleft", legend.horiz=TRUE, newpage=FALSE)

## End(Not run)

Pi documentation built on Nov. 26, 2020, 2:01 a.m.