Documentations
Training and Analysis functions
These functions are used for training and analysis

sPipeline
Function to setup the pipeline for completing ab initio training given the input data

sHexGrid
Function to define a suprahexagonal grid

sHexGridVariant
Function to define a variant of a suprahexagonal grid

sHexPolygon
Function to extract polygon location per hexagon within a suprahexagonal grid

sTopology
Function to define the topology of a map grid

sInitial
Function to initialise a sInit object given a topology and input data

sTrainology
Function to define trainology (training environment)

sTrainSeq
Function to implement training via sequential algorithm

sTrainBatch
Function to implement training via batch algorithm

sBMH
Function to identify the bestmatching hexagons/rectangles for the input data

sNeighDirect
Function to calculate direct neighbors for each hexagon/rectangle in a grid

sNeighAny
Function to calculate any neighbors for each hexagon/rectangle in a grid

sHexDist
Function to calculate distances between hexagons/rectangles in a 2D grid

sDistance
Function to compute the pairwise distance for a given data matrix

sDmat
Function to calculate distance matrix in highdimensional input space but according to neighborhood relationships in 2D output space

sDmatMinima
Function to identify local minima (in 2D output space) of distance matrix (in highdimensional input space)

sDmatCluster
Function to partition a grid map into clusters

sCompReorder
Function to reorder component planes

sWriteData
Function to write out the bestmatching hexagons and/or cluster bases in terms of data

sMapOverlay
Function to overlay additional data onto the trained map for viewing the distribution of that additional data
Visualisation functions
These functions are used for visualisation

visHexPattern
Function to visualise codebook matrix or input patterns within a suprahexagonal grid

visHexGrid
Function to visualise a suprahexagonal grid

visHexMapping
Function to visualise various mapping items within a suprahexagonal grid

visHexBarplot
Function to visualise codebook matrix using barplot for all hexagons or a specific one

visHexComp
Function to visualise a component plane of a suprahexagonal grid

visColormap
Function to define a colormap

visColoralpha
Function to add transparent (alpha) into colors

visColorbar
Function to define a colorbar

visVp
Function to create viewports for multiple suprahexagonal grids

visHexMulComp
Function to visualise multiple component planes of a suprahexagonal grid

visHexAnimate
Function to animate multiple component planes of a suprahexagonal grid

visCompReorder
Function to visualise multiple component planes reorded within a sheetshape rectangle grid

visDmatCluster
Function to visualise clusters/bases partitioned from a suprahexagonal grid

visDmatHeatmap
Function to visualise gene clusters/bases partitioned from a suprahexagonal grid using heatmap

visKernels
Function to visualize neighborhood kernels

visHeatmap
Function to visualise input data matrix using heatmap

visHeatmapAdv
Function to visualise input data matrix using advanced heatmap

visTreeBootstrap
Function to build and visualise the bootstrapped tree

visTreeBSclust
Function to obtain clusters from a bootstrapped tree
Builtin datasets

Fang
(Fang.sampleinfo, Fang.geneinfo)
Human embryo gene expression dataset from Fang et al. (2010)

Golub
Leukemia gene expression dataset from Golub et al. (1999)

Xiang
Arabidopsis embryo gene expression dataset from Xiang et al.