xVisEvidence | R Documentation

## Function to visualise evidence for prioritised genes in a gene network

### 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"
`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

`xPierMatrix`

### Examples

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

    ## End(Not run)
    RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev"
    ## 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)