# supraHex: a supra-hexagonal map for analysing tabular omics data

## Documentation for package ‘supraHex’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

Fang | Human embryo gene expression dataset from Fang et al. (2010)
Fang.geneinfo | Human embryo gene expression dataset from Fang et al. (2010)
Fang.sampleinfo | Human embryo gene expression dataset from Fang et al. (2010)
Golub | Leukemia gene expression dataset from Golub et al. (1999)
sBMH | Function to identify the best-matching hexagons/rectangles for the input data
sCompReorder | Function to reorder component planes
sDistance | Function to compute the pairwise distance for a given data matrix
sDmat | Function to calculate distance matrix in high-dimensional input space but according to neighborhood relationships in 2D output space
sDmatCluster | Function to partition a grid map into clusters
sDmatMinima | Function to identify local minima (in 2D output space) of distance matrix (in high-dimensional input space)
sHexDist | Function to calculate distances between hexagons/rectangles in a 2D grid
sHexGrid | Function to define a supra-hexagonal grid
sInitial | Function to initialise a sInit object given a topology and input data
sMapOverlay | Function to overlay additional data onto the trained map for viewing the distribution of that additional data
sNeighAny | Function to calculate any neighbors for each hexagon/rectangle in a grid
sNeighDirect | Function to calculate direct neighbors for each hexagon/rectangle in a grid
sPipeline | Function to setup the pipeline for completing ab initio training given the input data
sTopology | Function to define the topology of a map grid
sTrainBatch | Function to implement training via batch algorithm
sTrainology | Function to define trainology (training environment)
sTrainSeq | Function to implement training via sequential algorithm
sWriteData | Function to write out the best-matching hexagons and/or cluster bases in terms of data
visColoralpha | Function to add transparent (alpha) into colors
visColorbar | Function to define a colorbar
visColormap | Function to define a colormap
visCompReorder | Function to visualise multiple component planes reorded within a sheet-shape rectangle grid
visDmatCluster | Function to visualise clusters/bases partitioned from a supra-hexagonal grid
visDmatHeatmap | Function to visualise gene clusters/bases partitioned from a supra-hexagonal grid using heatmap
visHeatmap | Function to visualise input data matrix using heatmap
visHeatmapAdv | Function to visualise input data matrix using advanced heatmap
visHexAnimate | Function to animate multiple component planes of a supra-hexagonal 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 supra-hexagonal grid
visHexGrid | Function to visualise a supra-hexagonal grid
visHexMapping | Function to visualise various mapping items within a supra-hexagonal grid
visHexMulComp | Function to visualise multiple component planes of a supra-hexagonal grid
visHexPattern | Function to visualise codebook matrix or input patterns within a supra-hexagonal grid
visKernels | Function to visualize neighborhood kernels
visTreeBootstrap | Function to build and visualise the bootstrapped tree
visTreeBSclust | Function to obtain clusters from a bootstrapped tree
visVp | Function to create viewports for multiple supra-hexagonal grids
Xiang | Arabidopsis embryo gene expression dataset from Xiang et al. (2011)