bandle-plots-spatial: Generate a PCA plot with smoothed probability contours

In ococrook/bandle: An R package for the Bayesian analysis of differential subcellular localisation experiments

Generate a PCA plot with smoothed probability contours

Description

Generate a PCA plot with smoothed probability contours

Usage

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

 ## Not run: 
## 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)

## End(Not run)

ococrook/bandle documentation built on Nov. 4, 2024, 12:27 a.m.