plotOutliers: Generate trace and density plots for all chains

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

Generate trace and density plots for all chains

Description

This function takes the output from running bandle i.e. a bandleParams object and generates trace and density plots for each MCMC chain in each condition. The output plots can be used to help assess convergence of MCMC chains.

Usage

plotOutliers(params, auto.layout = TRUE)

Arguments

params	An instance of class bandleParams
auto.layout	A logical specifying whether to automatically determine the arrangement of each plot. Default is TRUE.

Value

Generates trace and density plots for each chain for each condition/experiment.

Examples

## 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 = 20L,
              burnin = 1L,
              thin = 2L,
              numChains = 2,
              BPPARAM = SerialParam(RNGseed = 1),
              seed = 1)

## Process the results
plotOutliers(res)

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