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


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Documentation for package ‘supraHex’ version 1.26.0

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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
sHexGridVariant Function to define a variant of a supra-hexagonal grid
sHexPolygon Function to extract polygon location per hexagon within 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)