xVisEvidenceAdv: Function to visualise evidence and priority scores for...

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

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, xGGnetwork, xPieplot

Examples

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)

Pi documentation built on Nov. 29, 2021, 3 p.m.