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

Description Usage Arguments Value See Also Examples

View source: R/xVisEvidenceAdv.r

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

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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

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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. 26, 2020, 2:01 a.m.