xVisEvidence | R Documentation |
xVisEvidence
is supposed to visualise evidence for prioritised
genes in a gene network. It returns an object of class "igraph".
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, ...)
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. |
a subgraph, an object of class "igraph".
xPierMatrix
## Not run: # Load the library library(Pi) ## End(Not run) RData.location <- "http://galahad.well.ox.ac.uk/bigdata" ## 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)