Produces a pca plot with uncertainty in organelle means projected onto the PCA plot with contours.
nicheMeans2D(
object,
params,
priors,
dims = c(1, 2),
fcol = "markers",
aspect = 0.5
)
A valid object of class MSnset
A valid object of class MCMCParams
that has been
processed and checked for convergence
The prior that were used in the model
The PCA dimension in which to project he data, default is
c(1,2)
The columns of the feature data which contain the marker data.
A argument to change the plotting aspect of the PCA
Used for side effect of producing plot. Invisibily returns an ggplot object that can be further manipulated
if (FALSE) {
library("pRolocdata")
data("tan2009r1")
tanres <- tagmMcmcTrain(object = tan2009r1)
tanres <- tagmMcmcProcess(tanres)
tan2009r1 <- tagmMcmcPredict(object = tan2009r1, params = tanres, probJoint = TRUE)
myparams <- chains(e14Tagm_converged_pooled)[[1]]
myparams2 <- chains(mcmc_pool_chains(tanres))[[1]]
priors <- tanres@priors
pRoloc:::nicheMeans2D(object = tan2009r1, params = myparams2, priors = priors)
}