sDmat: Function to calculate distance matrix in high-dimensional...

In hfang-bristol/supraHex: supraHex: a supra-hexagonal map for analysing tabular omics data

Description

sDmat is supposed to calculate distance (measured in high-dimensional input space) to neighbors (defined by based on 2D output space) for each of hexagons/rectangles

Usage

sDmat(sMap, which_neigh = 1, distMeasure = c("median", "mean", "min",
"max"))

Arguments

sMap	an object of class "sMap"
which_neigh	which neighbors in 2D output space are used for the calculation. By default, it sets to "1" for direct neighbors, and "2" for neighbors within neighbors no more than 2, and so on
distMeasure	distance measure used to calculate distances in high-dimensional input space

Value

• dMat: a vector with the length of nHex. It stores the distance a hexaon/rectangle is away from its output-space-defined neighbors in high-dimensional input space

Note

"which_neigh" is defined in output 2D space, but "distMeasure" is defined in high-dimensional input space

See Also

sNeighAny

Examples

# 1) generate an iid normal random matrix of 100x10 
data <- matrix( rnorm(100*10,mean=0,sd=1), nrow=100, ncol=10)

# 2) get trained using by default setup
sMap <- sPipeline(data=data)

# 3) calculate "median" distances in INPUT space to different neighbors in 2D OUTPUT space
# 3a) using direct neighbors in 2D OUTPUT space
dMat <- sDmat(sMap=sMap, which_neigh=1, distMeasure="median")
# 3b) using no more than 2-topological neighbors in 2D OUTPUT space
# dMat <- sDmat(sMap=sMap, which_neigh=2, distMeasure="median")

hfang-bristol/supraHex documentation built on May 24, 2021, 3:13 p.m.