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

Description Usage Arguments Value See Also Examples

View source: R/xVisEvidence.r

Description

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

Usage

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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

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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.