nicheMeans2D {pRoloc} | R Documentation

## Uncertainty plot organelle means

### Description

Produces a pca plot with uncertainty in organelle means projected onto the PCA plot with contours.

### Usage

    nicheMeans2D(object, params, priors, dims = c(1, 2), fcol = "markers",
      aspect = 0.5)

### Arguments

`object` | A valid object of class `MSnset`
`params` | A valid object of class `MCMCParams` that has been processed and checked for convergence
`priors` | The prior that were used in the model
`dims` | The PCA dimension in which to project he data, default is `c(1,2)`
`fcol` | The columns of the feature data which contain the marker data.
`aspect` | A argument to change the plotting aspect of the PCA

### Value

Used for side effect of producing plot. Invisibily returns an ggplot object that can be further manipulated

### Author(s)

Oliver M. Crook <omc25@cam.ac.uk>

### Examples

    ## Not run:
    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)

    ## End(Not run)

[Package pRoloc version 1.30.0 Index]