EmbedSOM {EmbedSOM} | R Documentation |
Process the cells with SOM into a nice embedding
EmbedSOM(fsom = NULL, smooth = NULL, k = NULL, adjust = NULL, data = NULL, map = NULL, importance = NULL, emcoords = "flat", emcoords.pow = 1)
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 SOM neighbors to take into the whole computation |
adjust |
How much non-local information to remove (parameter a) |
data |
Data matrix with points that optionally overrides the one from 'fsom$data'. |
map |
Map object in FlowSOM format, to optionally override 'fsom$map' |
importance |
Importance of dimensions that was used to train the SOM |
emcoords |
Either a matrix of embedded coordinates (same number of rows as map$coords, and either 2 or 3 columns depending on the SOM grid dimension), or one of 'flat' (default behavior), 'som' (adjust the SOM coords according to U-matrix distances), 'mst' (embed to MST-like structure), 'fsom-mst' (embed to MST that should look exactly like that of FlowSOM), 'tsne' (embed using tSNE from package Rtsne), 'umap' (embed using UMAP from package umap) or 'uwot::umap' (embed using UMAP from package uwot) |
emcoords.pow |
Exaggeration factor (power) of the distances in U-matrix used for some methods of auto-generating emcoords; default 1. |
matrix with 2D or 3D coordinates of the embedded cels, 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)