runNMDS {mia} | R Documentation |
Perform non-metric multi-dimensional scaling (nMDS) on samples, based on the
data in a SingleCellExperiment
object.
calculateNMDS(x, ...) ## S4 method for signature 'ANY' calculateNMDS( x, FUN = vegdist, nmdsFUN = c("isoMDS", "monoMDS"), ncomponents = 2, ntop = 500, subset_row = NULL, scale = FALSE, transposed = FALSE, keep_dist = FALSE, ... ) ## S4 method for signature 'SummarizedExperiment' calculateNMDS(x, ..., exprs_values = "counts", FUN = vegdist) ## S4 method for signature 'SingleCellExperiment' calculateNMDS( x, ..., exprs_values = "counts", dimred = NULL, n_dimred = NULL, FUN = vegdist ) runNMDS(x, ..., altexp = NULL, name = "NMDS") plotNMDS(x, ..., ncomponents = 2)
x |
For For |
... |
additional arguments to pass to |
FUN |
a |
nmdsFUN |
a |
ncomponents |
Numeric scalar indicating the number of NMDS dimensions to obtain. |
ntop |
Numeric scalar specifying the number of features with the highest variances to use for dimensionality reduction. |
subset_row |
Vector specifying the subset of features to use for dimensionality reduction. This can be a character vector of row names, an integer vector of row indices or a logical vector. |
scale |
Logical scalar, should the expression values be standardized? |
transposed |
Logical scalar, is x transposed with cells in rows? |
keep_dist |
Logical scalar indicating whether the |
exprs_values |
a single |
dimred |
String or integer scalar specifying the existing dimensionality reduction results to use. |
n_dimred |
Integer scalar or vector specifying the dimensions to use if dimred is specified. |
altexp |
String or integer scalar specifying an alternative experiment containing the input data. |
name |
String specifying the name to be used to store the result in the reducedDims of the output. |
Either MASS::isoMDS
or
vegan::monoMDS
are used internally to compute
the NMDS components. If you supply a custom FUN
, make sure that
the arguments of FUN
and nmdsFUN
do not collide.
For calculateNMDS
, a matrix is returned containing the MDS
coordinates for each sample (row) and dimension (column).
Felix Ernst
MASS::isoMDS
,
vegan::monoMDS
for NMDS component calculation.
plotMDS
, to quickly visualize the
results.
# generate some example data mat <- matrix(1:60, nrow = 6) df <- DataFrame(n = c(1:6)) se <- SummarizedExperiment(assays = list(counts = mat), rowData = df) # calculateNMDS(se) # data(esophagus) esophagus <- runNMDS(esophagus, FUN = vegan::vegdist, name = "BC") esophagus <- runNMDS(esophagus, FUN = vegan::vegdist, name = "euclidean", method = "euclidean") reducedDims(esophagus)