bdm.dMap: Class density maps

In jgarriga65/bigMap: Big Data Mapping

Class density maps

Description

Compute the class density maps of a set of classes on the embedding grid. This function returns a fuzzy mapping of the set of classes on the grid cells. The classes can be whatever set of classes of interest and must be given as a vector of point-wise discrete labels (either numeric, string or factor).

Usage

bdm.dMap(bdm, data = NULL, threads = 2, mpi.cl = NULL, layer = 1)

Arguments

bdm	A bdm instance as generated by bdm.init().
data	A vector of discret covariates or class labels. The covariate values can be of any factorizable type. By default (data=NULL) the function computes the density maps based on the clustering labels (i.e. equivalent to data=bdm.labels(bdm))
threads	Number of parallel threads (according to data size and hardware resources, i.e. number of cores and available memory. Default value is threads = 4).
mpi.cl	MPI (inter-node parallelization) cluster as generated by bdm.mpi.start(). (By default mpi.cl = NULL a 'SOCK' (intra-node parallelization) cluster is generated).
layer	The number of the t-SNE layer (1 by default).

Details

bdm.dMap() computes the join distribution P(V=v_{i},C=c_{j}) where V={v_{1},\dots,v_{l}} is the discrete covariate and C={c_{1},\dots, c_{g}} are the grid cells of the paKDE raster. That is, this function recomputes the paKDE but keeping track of the covariate (or class) label of each data-point. This results in a fuzzy distribution of the covariate (class) at each cell.

Usually, figuring out the join distribution P(V=v_{i},C=c_{j}) entails an intensive computation. Thus bdm.dMap() performs the computation and stores the result in a dedicated element named $dMap. Afterwards the class density maps can be visualized with the bdm.dMap.plot() function.

Value

A copy of the input bdm instance with element $dMap, a matrix with a soft clustering of the grid cells.

Examples

# --- load example dataset
bdm.example()
## Not run: 
m <- bdm.dMap(ex$map, threads = 4)

## End(Not run)

jgarriga65/bigMap documentation built on June 10, 2024, 7:05 a.m.