xVisEvidenceAdv | R Documentation

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

### Description

`xVisEvidenceAdv` is supposed to visualise evidence and priority scores for prioritised genes in a gene network. It returns an object of class "ggplot".

### Usage

    xVisEvidenceAdv(xTarget, g = NA, nodes = NULL, node.info = c("smart",
    "none"), neighbor.order = 1, neighbor.seed = TRUE,
    neighbor.top = NULL, largest.comp = TRUE, node.label.size = 2,
    node.label.color = "black", node.label.alpha = 0.9,
    node.label.padding = 0.5, node.label.arrow = 0,
    node.label.force = 0.1, node.shape = 19,
    node.color.title = "Pi\nrating", colormap = "white-yellow-red",
    ncolors = 64, zlim = c(0, 5), node.size.range = 5, title = "",
    edge.color = "orange", edge.color.alpha = 0.5, edge.curve = 0,
    edge.arrow.gap = 0.025, pie.radius = NULL, pie.color = "black",
    pie.color.alpha = 1, pie.thick = 0.1, ...)

### 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
`node.label.size` | a vector specifying node size or a character specifying which node attribute used for node label size
`node.label.color` | the node label color
`node.label.alpha` | the 0-1 value specifying transparency of node labelling
`node.label.padding` | the padding around the labeled node
`node.label.arrow` | the arrow pointing to the labeled node
`node.label.force` | the repelling force between overlapping labels
`node.shape` | an integer specifying node shape
`node.color.title` | a character specifying the title for node coloring
`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
`ncolors` | the number of colors specified over the colormap
`zlim` | the minimum and maximum values for which colors should be plotted
`node.size.range` | the range of actual node size
`title` | a character specifying the title for the plot
`edge.color` | a character specifying the edge colors
`edge.color.alpha` | the 0-1 value specifying transparency of edge colors
`edge.curve` | a numeric value specifying the edge curve. 0 for the straight line
`edge.arrow.gap` | a gap between the arrow and the node
`pie.radius` | the radius of a pie. If NULL, it equals roughly 1/75
`pie.color` | the border color of a pie
`pie.color.alpha` | the 0-1 value specifying transparency of pie border colors
`pie.thick` | the pie border thickness
`...` | additional graphic parameters for xGGnetwork

### Value

a ggplot object.

### See Also

`xVisEvidence`

### Examples

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

    ## End(Not run)
    RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
    ## Not run:
    ## TNFRSF1A
    xVisEvidenceAdv(xTarget, nodes="TNFRSF1A", neighbor.order=1,
    neighbor.seed=TRUE, neighbor.top=NULL)

    ## End(Not run)