Wrapper fonctions to create plots for specific types
of reduced dimension results produced by the various fmsne
dimensionality reductions. The function follow the scater
package's syntax.
plotMSSNE(object, ..., ncomponents = 2)
plotFMSSNE(object, ..., ncomponents = 2)
plotFMSTSNE(object, ..., ncomponents = 2)
plotMSTSNE(object, ..., ncomponents = 2)A SingleCellExperiment object.
Additional arguments to pass to
scater::plotReducedDim().
numeric(1) indicating the number of
dimensions components to plot This can also be a numeric
vector, see scater::plotReducedDim() for details.
A ggplot object.
As for the equivalent functions from the scater package, each
function is a convenient wrapper around scater::plotReducedDim()
that searches the SingleCellExperiment::reducedDims() slot for
an appropriately named dimensionality reduction result:
"FMSTSNE" for plotFMSTNSE()
"FMSSNE" for plotFMSNSE()
"MSTSNE" for plotMSTNSE()
"MSTSNE" for plotMSNSE()
Its only purpose is to streamline workflows to avoid the need to specify the ‘dimred’ argument.
runFMSSNE(), runFMSSNE(), runMSTSNE() and runMSSNE() for
the functions that actually perform the calculations.
scater::plotReducedDim() for the underlying plotting function.