EmbedSOM | R Documentation |
Process the cells with SOM into a nice embedding
EmbedSOM( data = NULL, map = NULL, fsom = NULL, smooth = NULL, k = NULL, adjust = NULL, importance = NULL, coordsFn = NULL, coords = NULL, emcoords = NULL, emcoords.pow = 1, parallel = F, threads = if (parallel) 0 else 1 )
data |
Data matrix with points that optionally overrides the one from |
map |
Map object in FlowSOM format, to optionally override |
fsom |
FlowSOM object with a built SOM (used if data or map are missing) |
smooth |
Produce smoother (positive values) or more rough approximation (negative values). |
k |
How many neighboring landmarks (e.g. SOM nodes) to take into the whole computation |
adjust |
How much non-local information to remove from the approximation |
importance |
Scaling of the landmarks, will be used to scale the incoming data (should be same as used for training the SOM or to select the landmarks) |
coordsFn |
A coordinates-generating function (e.g. |
coords |
A matrix of embedding-space coordinates that correspond to |
emcoords |
Provided for backwards compatibility, will be removed. Use |
emcoords.pow |
Provided for backwards compatibility, will be removed. Use a parametrized |
parallel |
Boolean flag whether the computation should be parallelized (this flag is just a nice name for |
threads |
Number of threads used for computation, 0 chooses hardware concurrency, 1 (default) turns off parallelization. |
matrix with 2D or 3D coordinates of the embedded data
, depending on the map
d <- cbind(rnorm(10000), 3*runif(10000), rexp(10000)) colnames(d) <- paste0("col",1:3) map <- EmbedSOM::SOM(d, xdim=10, ydim=10) e <- EmbedSOM::EmbedSOM(data=d, map=map) EmbedSOM::PlotEmbed(e, data=d, 'col1', pch=16)
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