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.

Author
Hai Fang and Julian Gough
Date of publication
2016-06-25 16:53:43
Maintainer
Hai Fang <hfang@well.ox.ac.uk>
License
GPL-2
Version
1.11.1
URLs

View on R-Forge

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/content-cite.html
supraHex/inst/staticdocs/templates/content-demo.html
supraHex/inst/staticdocs/templates/content-demos.html
supraHex/inst/staticdocs/templates/content-docs.html
supraHex/inst/staticdocs/templates/content-index.html
supraHex/inst/staticdocs/templates/content-install.html
supraHex/inst/staticdocs/templates/content-topic.html
supraHex/inst/staticdocs/templates/footer.html
supraHex/inst/staticdocs/templates/head.html
supraHex/inst/staticdocs/templates/header.html
supraHex/inst/staticdocs/templates/layout.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/nohup.out
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