plotNetwork {BayesSUR} | R Documentation |
plot network representation of the associations between responses and predictors
Description
Plot the network representation of the associations between responses and predictors, based on the estimated gamma matrix and graph of responses from a "BayesSUR" class object.
Usage
plotNetwork(
x,
includeResponse = NULL,
excludeResponse = NULL,
includePredictor = NULL,
excludePredictor = NULL,
MatrixGamma = NULL,
PmaxPredictor = 0.5,
PmaxResponse = 0.5,
nodesizePredictor = 2,
nodesizeResponse = 15,
no.isolates = FALSE,
lineup = 1.2,
gray.alpha = 0.6,
edgewith.response = 5,
edgewith.predictor = 2,
edge.weight = FALSE,
label.predictor = NULL,
label.response = NULL,
color.predictor = NULL,
color.response = NULL,
name.predictors = NULL,
name.responses = NULL,
vertex.frame.color = NA,
layoutInCircle = FALSE,
header = "",
...
)
Arguments
x |
an object of class |
includeResponse |
A vector of the response names which are shown in the network |
excludeResponse |
A vector of the response names which are not shown in the network |
includePredictor |
A vector of the predictor names which are shown in the network |
excludePredictor |
A vector of the predictor names which are not shown in the network |
MatrixGamma |
A matrix or dataframe of the latent indicator variable.
Default is |
PmaxPredictor |
cutpoint for thresholding the estimated latent indicator variable. Default is 0.5 |
PmaxResponse |
cutpoint for thresholding the learning structure matrix of multiple response variables. Default is 0.5 |
nodesizePredictor |
node size of Predictors in the output graph. Default is 15 |
nodesizeResponse |
node size of response variables in the output graph. Default is 25 |
no.isolates |
remove isolated nodes from responses graph and full graph, may get problem if there are also isolated Predictors |
lineup |
A ratio of the heights between responses' area and predictors' |
gray.alpha |
the opacity. The default is 0.6 |
edgewith.response |
the edge width between response nodes |
edgewith.predictor |
the edge width between the predictor and response node |
edge.weight |
draw weighted edges after thresholding at 0.5. The
default value |
label.predictor |
A vector of the names of predictors |
label.response |
A vector of the names of response variables |
color.predictor |
color of the predictor nodes |
color.response |
color of the response nodes |
name.predictors |
A subtitle for the predictors |
name.responses |
A subtitle for the responses |
vertex.frame.color |
color of the frame of the vertices. If you don't want vertices to have a frame, supply NA as the color name |
layoutInCircle |
place vertices on a circle, in the order of their
vertex ids. The default is |
header |
the main title |
... |
other arguments |
Examples
data("exampleEQTL", package = "BayesSUR")
hyperpar <- list(a_w = 2, b_w = 5)
set.seed(9173)
fit <- BayesSUR(
Y = exampleEQTL[["blockList"]][[1]],
X = exampleEQTL[["blockList"]][[2]],
data = exampleEQTL[["data"]], outFilePath = tempdir(),
nIter = 10, burnin = 0, nChains = 1, gammaPrior = "hotspot",
hyperpar = hyperpar, tmpFolder = "tmp/"
)
## check output
# draw network representation of the associations between responses and covariates
plotNetwork(fit)