pRoloc (version 1.12.3)

SpatProtVis-class: 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.

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)