xVisEvidenceAdv | R Documentation |
xVisEvidenceAdv
is supposed to visualise evidence and priority
scores for prioritised genes in a gene network. It returns an object of
class "ggplot".
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, ...)
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 |
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 |
a ggplot object.
xVisEvidence
## 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)