Runs t-SNE on the aligned cell factors (result from
alignFactors
), or unaligned cell factors (result from
runIntegration
)) to generate a 2D embedding for visualization.
By default Rtsne
(Barnes-Hut implementation of t-SNE)
method is invoked, while alternative "fftRtsne" method (FFT-accelerated
Interpolation-based t-SNE, using Kluger Lab implementation) is also
supported. For very large datasets, it is recommended to use
method = "fftRtsne"
due to its efficiency and scalability.
Extra external installation steps are required for using "fftRtsne" method. Please consult detailed guide.
Usage
runTSNE(
object,
useRaw = NULL,
useDims = NULL,
nDims = 2,
usePCA = FALSE,
perplexity = 30,
theta = 0.5,
method = c("Rtsne", "fftRtsne"),
dimredName = "TSNE",
asDefault = NULL,
fitsnePath = NULL,
seed = 42,
verbose = getOption("ligerVerbose", TRUE),
k = nDims,
use.raw = useRaw,
dims.use = useDims,
use.pca = usePCA,
fitsne.path = fitsnePath,
rand.seed = seed
)
Arguments
- object
liger object with factorization results.
- useRaw
Whether to use un-aligned cell factor loadings (\(H\) matrices). Default
NULL
search for aligned factor loadings first and un-aligned loadings then.- useDims
Index of factors to use for computing the embedding. Default
NULL
uses all factors.- nDims
Number of dimensions to reduce to. Default
2
.- usePCA
Whether to perform initial PCA step for Rtsne. Default
FALSE
.- perplexity
Numeric parameter to pass to Rtsne (expected number of neighbors). Default
30
.- theta
Speed/accuracy trade-off (increase for less accuracy), set to
0.0
for exact TSNE. Default0.5
.- method
Choose from
"Rtsne"
or"fftRtsne"
. See Description. Default"Rtsne"
.- dimredName
Name of the variable in
cellMeta
slot to store the result matrix. Default"TSNE"
.- asDefault
Logical, whether to set the resulting dimRed as default for visualization. Default
NULL
will set it when no default is set.- fitsnePath
Path to the cloned FIt-SNE directory (i.e.
'/path/to/dir/FIt-SNE'
). Required only when first time usingrunTSNE
withmethod = "fftRtsne"
. DefaultNULL
.- seed
Random seed for reproducibility. Default
42
.- verbose
Logical. Whether to show information of the progress. Default
getOption("ligerVerbose")
orTRUE
if users have not set.- use.raw, dims.use, k, use.pca, fitsne.path, rand.seed
Deprecated. See Usage section for replacement.
Value
The object
where a "TSNE"
variable is updated in the
cellMeta
slot with the whole 2D embedding matrix.