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

A supra-hexagonal map is a giant hexagon on a 2-dimensional grid seamlessly consisting of smaller hexagons. It is supposed to train, analyse and visualise a high-dimensional omics input data. The supraHex is able to carry out gene clustering/meta-clustering and sample correlation, plus intuitive visualisations to facilitate exploratory analysis. More importantly, it allows for overlaying additional data onto the trained map to explore relations between input and additional data. So with supraHex, it is also possible to carry out multilayer omics data comparisons. Newly added utilities are advanced heatmap visualisation and tree-based analysis of sample relationships. Uniquely to this package, users can ultrafastly understand any tabular omics data, both scientifically and artistically, especially in a sample-specific fashion but without loss of information on large genes.

AuthorHai Fang and Julian Gough
Date of publicationNone
MaintainerHai Fang <hfang@well.ox.ac.uk>
LicenseGPL-2
Version1.12.0
http://suprahex.r-forge.r-project.org

View on Bioconductor

Man pages

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

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....

Files in this package

supraHex/DESCRIPTION
supraHex/NAMESPACE
supraHex/R
supraHex/R/sBMH.r
supraHex/R/sCompReorder.r
supraHex/R/sDistance.r
supraHex/R/sDmat.r
supraHex/R/sDmatCluster.r
supraHex/R/sDmatMinima.r
supraHex/R/sHexDist.r
supraHex/R/sHexGrid.r
supraHex/R/sInitial.r
supraHex/R/sMapOverlay.r
supraHex/R/sNeighAny.r
supraHex/R/sNeighDirect.r
supraHex/R/sPipeline.r
supraHex/R/sTopology.r
supraHex/R/sTrainBatch.r
supraHex/R/sTrainSeq.r
supraHex/R/sTrainology.r
supraHex/R/sWriteData.r
supraHex/R/visColoralpha.r
supraHex/R/visColorbar.r
supraHex/R/visColormap.r
supraHex/R/visCompReorder.r
supraHex/R/visDmatCluster.r
supraHex/R/visDmatHeatmap.r
supraHex/R/visHeatmap.r
supraHex/R/visHeatmapAdv.r
supraHex/R/visHexAnimate.r
supraHex/R/visHexBarplot.r
supraHex/R/visHexComp.r
supraHex/R/visHexGrid.r
supraHex/R/visHexMapping.r
supraHex/R/visHexMulComp.r
supraHex/R/visHexPattern.r
supraHex/R/visKernels.r
supraHex/R/visTreeBSclust.r
supraHex/R/visTreeBootstrap.r
supraHex/R/visVp.r
supraHex/build
supraHex/build/vignette.rds
supraHex/data
supraHex/data/Fang.RData
supraHex/data/Golub.RData
supraHex/data/Xiang.RData
supraHex/data/datalist
supraHex/inst
supraHex/inst/CITATION
supraHex/inst/NEWS
supraHex/inst/doc
supraHex/inst/doc/supraHex_vignettes.R
supraHex/inst/doc/supraHex_vignettes.Rnw
supraHex/inst/doc/supraHex_vignettes.pdf
supraHex/inst/staticdocs
supraHex/inst/staticdocs/CITATIONs.md
supraHex/inst/staticdocs/INSTALLATIONs.md
supraHex/inst/staticdocs/INSTALLATIONs_pre.md
supraHex/inst/staticdocs/README.md
supraHex/inst/staticdocs/README_previous.md
supraHex/inst/staticdocs/demo
supraHex/inst/staticdocs/demo/Fang.r
supraHex/inst/staticdocs/demo/Golub.r
supraHex/inst/staticdocs/demo/Hiratani.r
supraHex/inst/staticdocs/demo/ISMB2014.r
supraHex/inst/staticdocs/demo/List_demos.txt
supraHex/inst/staticdocs/demo/PyClone.r
supraHex/inst/staticdocs/demo/RNAseq.r
supraHex/inst/staticdocs/demo/Sardar.r
supraHex/inst/staticdocs/demo/Xiang.r
supraHex/inst/staticdocs/docs.r
supraHex/inst/staticdocs/faq
supraHex/inst/staticdocs/faq/FAQ1.r
supraHex/inst/staticdocs/faq/FAQ2.r
supraHex/inst/staticdocs/faq/FAQ3.r
supraHex/inst/staticdocs/faq/FAQ4.r
supraHex/inst/staticdocs/faq/FAQ5.r
supraHex/inst/staticdocs/faq/FAQ6.r
supraHex/inst/staticdocs/faq/FAQ7.r
supraHex/inst/staticdocs/faq/List_faqs.txt
supraHex/inst/staticdocs/images
supraHex/inst/staticdocs/images/supraHex_logo.png
supraHex/inst/staticdocs/images/supraHex_workflow.png
supraHex/inst/staticdocs/templates
supraHex/inst/staticdocs/templates/footer.html
supraHex/inst/staticdocs/templates/navbar.html
supraHex/man
supraHex/man/Fang.Rd supraHex/man/Golub.Rd supraHex/man/Xiang.Rd supraHex/man/sBMH.Rd supraHex/man/sCompReorder.Rd supraHex/man/sDistance.Rd supraHex/man/sDmat.Rd supraHex/man/sDmatCluster.Rd supraHex/man/sDmatMinima.Rd supraHex/man/sHexDist.Rd supraHex/man/sHexGrid.Rd supraHex/man/sInitial.Rd supraHex/man/sMapOverlay.Rd supraHex/man/sNeighAny.Rd supraHex/man/sNeighDirect.Rd supraHex/man/sPipeline.Rd supraHex/man/sTopology.Rd supraHex/man/sTrainBatch.Rd supraHex/man/sTrainSeq.Rd supraHex/man/sTrainology.Rd supraHex/man/sWriteData.Rd supraHex/man/visColoralpha.Rd supraHex/man/visColorbar.Rd supraHex/man/visColormap.Rd supraHex/man/visCompReorder.Rd supraHex/man/visDmatCluster.Rd supraHex/man/visDmatHeatmap.Rd supraHex/man/visHeatmap.Rd supraHex/man/visHeatmapAdv.Rd supraHex/man/visHexAnimate.Rd supraHex/man/visHexBarplot.Rd supraHex/man/visHexComp.Rd supraHex/man/visHexGrid.Rd supraHex/man/visHexMapping.Rd supraHex/man/visHexMulComp.Rd supraHex/man/visHexPattern.Rd supraHex/man/visKernels.Rd supraHex/man/visTreeBSclust.Rd supraHex/man/visTreeBootstrap.Rd supraHex/man/visVp.Rd
supraHex/vignettes
supraHex/vignettes/supraHex_vignettes-embryo.pdf
supraHex/vignettes/supraHex_vignettes-leukemia.pdf
supraHex/vignettes/supraHex_vignettes-plant.pdf
supraHex/vignettes/supraHex_vignettes-sMap_bu.pdf
supraHex/vignettes/supraHex_vignettes-sMap_cu.pdf
supraHex/vignettes/supraHex_vignettes-sMap_ep.pdf
supraHex/vignettes/supraHex_vignettes-sMap_ga.pdf
supraHex/vignettes/supraHex_vignettes-sMap_gm.pdf
supraHex/vignettes/supraHex_vignettes-sReorder.pdf
supraHex/vignettes/supraHex_vignettes.Rnw
supraHex/vignettes/supraHex_vignettes.bib

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