R/getTSNE.R
getTSNE.Rd
Run t-SNE dimensionality reduction method on a SingleCellExperiment Object
getTSNE(
inSCE,
useAssay = "logcounts",
useAltExp = NULL,
useReducedDim = NULL,
reducedDimName = "TSNE",
nIterations = 1000,
perplexity = 30,
run_pca = TRUE,
ntop = NULL,
seed = NULL
)
Input SingleCellExperiment object.
Assay to use for tSNE computation. If useAltExp
is
specified, useAssay
has to exist in
assays(altExp(inSCE, useAltExp))
. Default "logcounts"
The subset to use for tSNE computation, usually for the
selected.variable features. Default NULL
.
The low dimension representation to use for UMAP
computation. Default NULL
.
a name to store the results of the dimension
reductions. Default "TSNE"
.
maximum iterations. Default 1000
.
perplexity parameter. Default 30
.
run tSNE on PCA components? Default TRUE
.
Number of top features to use as a further variable feature
selection. Default NULL
.
Random seed for reproducibility of tSNE results.
Default NULL
will use global seed in use by the R environment.
A SingleCellExperiment object with tSNE computation
updated in reducedDim(inSCE, reducedDimName)
.