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

Fang | 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... |

sCompReorder | Function to reorder component planes |

sDistance | Function to compute the pairwise distance for a given data... |

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

sDmatCluster | Function to partition a grid map into clusters |

sDmatMinima | Function to identify local minima (in 2D output space) of... |

sHexDist | Function to calculate distances between hexagons/rectangles... |

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... |

sInitial | Function to initialise a sInit object given a topology and... |

sMapOverlay | Function to overlay additional data onto the trained map for... |

sNeighAny | Function to calculate any neighbors for each... |

sNeighDirect | Function to calculate direct neighbors for each... |

sPipeline | Function to setup the pipeline for completing ab initio... |

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... |

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... |

visDmatCluster | Function to visualise clusters/bases partitioned from a... |

visDmatHeatmap | Function to visualise gene clusters/bases partitioned from a... |

visHeatmap | Function to visualise input data matrix using heatmap |

visHeatmapAdv | Function to visualise input data matrix using advanced... |

visHexAnimate | Function to animate multiple component planes of a... |

visHexBarplot | Function to visualise codebook matrix using barplot for all... |

visHexComp | Function to visualise a component plane of a supra-hexagonal... |

visHexGrid | Function to visualise a supra-hexagonal grid |

visHexMapping | Function to visualise various mapping items within a... |

visHexMulComp | Function to visualise multiple component planes of a... |

visHexPattern | Function to visualise codebook matrix or input patterns... |

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... |

Xiang | Arabidopsis embryo gene expression dataset from Xiang et al.... |

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