Generate a violin plot showing the probabilitiy of protein localisation to different organelles

Source: R/bandle-plots.R

These functions implement plotting functions for bandle objects

mcmc_plot_probs(
  params,
  fname,
  cond = 1,
  n = 1,
  bw = 0.05,
  scale = "width",
  trim = TRUE
)

Arguments

params

An instance of class bandleParams

fname

The name of the protein to plot

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.

bw

The bandwidth use in probability distribution smoothing of geom_violin Default is 0.05.

scale

Scaling of geom_violin. Defaults to width.

trim

trim parameter of geom_violin. Defaults to true.

Value

returns a named vector of differential localisation probabilities

Examples

library(pRolocdata)
data("tan2009r1")
set.seed(1)
tansim <- sim_dynamic(object = tan2009r1, 
                    numRep = 6L,
                   numDyn = 100L)
gpParams <- lapply(tansim$lopitrep, function(x) 
fitGPmaternPC(x, hyppar = matrix(c(0.5, 1, 100), nrow = 1)))
d1 <- tansim$lopitrep
control1 <- d1[1:3]
treatment1 <- d1[4:6]
mcmc1 <- bandle(objectCond1 = control1,
 objectCond2 = treatment1, gpParams = gpParams,
 fcol = "markers", numIter = 5L, burnin = 1L, thin = 2L,
 numChains = 1, BPPARAM = SerialParam(RNGseed = 1))
#> You haven't provided a seed, you may wish to provide a seed
#> 
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mcmc_plot_probs(params = mcmc1, fname = rownames(tan2009r1)[1])