Generate a PCA plot with smoothed probability contours

spatial2D(
  object,
  params,
  fcol = "markers",
  dims = c(1, 2),
  cov.function = NULL,
  theta = 2,
  derivative = 2,
  k = 1,
  cond = 1,
  n = 1,
  breaks = c(0.99, 0.95, 0.9, 0.85, 0.8, 0.75, 0.7),
  aspect = 0.5
)

Arguments

object: An instance of class MSnSet to provide the pca coordinates
params: An instance of class bandleParams
fcol: Feature columns that defines the markers. Defaults to "markers".
dims: The PCA dimensions to plot. Defaults to c(1,2)
cov.function: The covariance function for the smoothing kernel. Defaults to wendland.cov
theta: The theta parameter of the wendland.cov. Defaults to 2.
derivative: The derivative paramter of the wendland.cov. Defaults to 2.
k: The k parameter of the wendland.cov
cond: Which conditions do we want to plot. Must be 1 or 2. Default is 1
n: The chain from which we plot the probability distribution. Default is 1.
breaks: The levels at which to plot the contours. Defaults to c(0.99, 0.95, 0.9, 0.85, 0.8, 0.75, 0.7)
aspect: The aspect ratio of the pca plots. Defaults to 0.5.

Value

returns a named vector of differential localisation probabilities

Examples

 if (FALSE) {
## Generate some example data
library("pRolocdata")
data("tan2009r1")
set.seed(1)
tansim <- sim_dynamic(object = tan2009r1, 
                      numRep = 4L,
                      numDyn = 100L)
data <- tansim$lopitrep
control <- data[1:2]
treatment <- data[3:4]

## fit GP params
gpParams <- lapply(tansim$lopitrep, function(x) 
fitGPmaternPC(x, hyppar = matrix(c(0.5, 1, 100), nrow = 1)))

## run bandle
res <- bandle(objectCond1 = control,
              objectCond2 = treatment, 
              gpParams = gpParams,
              fcol = "markers",  
              numIter = 5L, 
              burnin = 1L, 
              thin = 2L,
              numChains = 1, 
              BPPARAM = SerialParam(RNGseed = 1),
              seed = 1)
               
## Process the results
bandleres <- bandleProcess(res)

## plot the results
spatial2D(control[[1]], bandleres)
}