SpatProtVis-class {pRoloc} | R Documentation

## Class `SpatProtVis`

### Description

A class for spatial proteomics visualisation, that upon instantiation, pre-computes all defined visualisations. Objects can be created with the `SpatProtVis` constructor and visualised with the `plot` method.

The class is essentially a wrapper around several calls to `plot2D` that stores the dimensionality reduction outputs, and is likely to be updated in the future.

### Usage

    SpatProtVis(x, methods, dims, methargs, ...)

### Arguments

`x` | An instance of class `MSnSet` to visualise.
`methods` | Dimensionality reduction methods to be used to visualise the data. Must be contained in `plot2Dmethods` (except `"scree"`). See `plot2D` for details.
`dims` | A list of numerics defining dimensions used for plotting. Default are `1` and `2`. If provided, the length of this list must be identical to the length of `methods`.
`methargs` | A list of additional arguments to be passed for each visualisation method. If provided, the length of this list must be identical to the length of `methods`.
`...` | Additional arguments. Currently ignored.

### Slots

`vismats`:

  A `"list"` of matrices containing the feature projections in 2 dimensions.

`data`:

  The original spatial proteomics data stored as an `"MSnSet"`.

`methargs`:

  A `"list"` of additional plotting arguments.

`objname`:

  A `"character"` defining how to name the dataset. By default, this is set using the variable name used at object creation.

### Methods

`plot`:

  Generates the figures for the respective `methods` and additional arguments defined in the constructor. If used in an interactive session, the user is prompted to press 'Return' before new figures are displayed.

`show`:

  A simple textual summary of the object.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>

### See Also

The data for the individual visualisations is created by `plot2D`.

### Examples

    library("pRolocdata")
    data(dunkley2006)
    ## Default parameters for a set of methods
    ## (in the interest of time, don't use t-SNE)
    m <- c("PCA", "MDS", "kpca")
    vis <- SpatProtVis(dunkley2006, methods = m)
    vis
    plot(vis)
    plot(vis, legend = "topleft")

    ## Setting method arguments
    margs <- c(list(kpar = list(sigma = 0.1)),
               list(kpar = list(sigma = 1.0)),
               list(kpar = list(sigma = 10)),
               list(kpar = list(sigma = 100)))
    vis <- SpatProtVis(dunkley2006,
                       methods = rep("kpca", 4),
                       methargs = margs)
    par(mfrow = c(2, 2))
    plot(vis)

    ## Multiple PCA plots but different PCs
    dims <- list(c(1, 2), c(3, 4))
    vis <- SpatProtVis(dunkley2006, methods = c("PCA", "PCA"), dims = dims)
    plot(vis)

[Package pRoloc version 1.26.0 Index]