R/plotting-ellipse.R
plotEllipse.Rd
Note that when running PCA, this function does not scale the data (centring is performed), as opposed to [plot2D()]. Only marker proteins are displayed; the protein of unknown location, that are not used to estimate the MAP parameters, are filtered out.
plotEllipse(object, params, dims = c(1, 2), method = "MAP", ...)
An [`MSnbase::MSnset`] containing quantitative spatial proteomics data.
An [`MAPParams`] with the TAGM-MAP parameters, as generated by `tagmMapTrain`.
A `numeric(2)` with the principal components along which to project the data. Default is `c(1, 2)`.
The method used. Currently `"MAP"` only.
Additional parameters passed to [plot2D()].
A PCA plot of the marker data with probability ellipises. The outer ellipse contains 99
probability whilst the middle and inner ellipses contain 95
and 90
clusters are represented by black circumpunct (circled dot).
[plot2D()] to visualise spatial proteomics data using various dimensionality reduction methods. For details about TAGM models, see [tagmPredict()] and the *pRoloc-bayesian* vignette.