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) |