supraHex: supraHex: a supra-hexagonal map for analysing tabular omics data
Version 1.13.3

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
Bioconductor views Clustering GeneExpression Software Visualization
Date of publication2017-03-27 18:10:08
MaintainerHai Fang <hfang@well.ox.ac.uk>
LicenseGPL-2
Version1.13.3
URL http://suprahex.r-forge.r-project.org
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("supraHex", repos="http://R-Forge.R-project.org")

Popular man pages

Fang: Human embryo gene expression dataset from Fang et al. (2010)
Golub: Leukemia gene expression dataset from Golub et al. (1999)
sDmatMinima: Function to identify local minima (in 2D output space) of...
sTopology: Function to define the topology of a map grid
visColorbar: Function to define a colorbar
visHexBarplot: Function to visualise codebook matrix using barplot for all...
visKernels: Function to visualize neighborhood kernels
See all...

All man pages Function index File listing

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
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....

Functions

Fang Man page
Fang.geneinfo Man page
Fang.sampleinfo Man page
Golub Man page
Xiang Man page
sBMH Man page Source code
sCompReorder Man page Source code
sDistance Man page Source code
sDmat Man page Source code
sDmatCluster Man page Source code
sDmatMinima Man page Source code
sHexDist Man page Source code
sHexGrid Man page Source code
sHexGridVariant Man page Source code
sHexPolygon Man page Source code
sInitial Man page Source code
sMapOverlay Man page Source code
sNeighAny Man page Source code
sNeighDirect Man page Source code
sPipeline Man page Source code
sTopology Man page Source code
sTrainBatch Man page Source code
sTrainSeq Man page Source code
sTrainology Man page Source code
sWriteData Man page Source code
visColoralpha Man page Source code
visColorbar Man page Source code
visColormap Man page Source code
visCompReorder Man page Source code
visDmatCluster Man page Source code
visDmatHeatmap Man page Source code
visHeatmap Man page Source code
visHeatmapAdv Man page Source code
visHexAnimate Man page Source code
visHexBarplot Man page Source code
visHexComp Man page Source code
visHexGrid Man page Source code
visHexMapping Man page Source code
visHexMulComp Man page Source code
visHexPattern Man page Source code
visKernels Man page Source code
visTreeBSclust Man page Source code
visTreeBootstrap Man page Source code
visVp Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/sBMH.r
R/sCompReorder.r
R/sDistance.r
R/sDmat.r
R/sDmatCluster.r
R/sDmatMinima.r
R/sHexDist.r
R/sHexGrid.r
R/sHexGridVariant.r
R/sHexPolygon.r
R/sInitial.r
R/sMapOverlay.r
R/sNeighAny.r
R/sNeighDirect.r
R/sPipeline.r
R/sTopology.r
R/sTrainBatch.r
R/sTrainSeq.r
R/sTrainology.r
R/sWriteData.r
R/visColoralpha.r
R/visColorbar.r
R/visColormap.r
R/visCompReorder.r
R/visDmatCluster.r
R/visDmatHeatmap.r
R/visHeatmap.r
R/visHeatmapAdv.r
R/visHexAnimate.r
R/visHexBarplot.r
R/visHexComp.r
R/visHexGrid.r
R/visHexMapping.r
R/visHexMulComp.r
R/visHexPattern.r
R/visKernels.r
R/visTreeBSclust.r
R/visTreeBootstrap.r
R/visVp.r
build
build/vignette.rds
data
data/Fang.RData
data/Golub.RData
data/Xiang.RData
data/datalist
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/supraHex_vignettes.R
inst/doc/supraHex_vignettes.Rnw
inst/doc/supraHex_vignettes.pdf
inst/staticdocs
inst/staticdocs/CITATIONs.md
inst/staticdocs/INSTALLATIONs.md
inst/staticdocs/INSTALLATIONs_pre.md
inst/staticdocs/README.md
inst/staticdocs/README_previous.md
inst/staticdocs/demo
inst/staticdocs/demo/Fang.r
inst/staticdocs/demo/Golub.r
inst/staticdocs/demo/Hiratani.r
inst/staticdocs/demo/ISMB2014.r
inst/staticdocs/demo/List_demos.txt
inst/staticdocs/demo/PyClone.r
inst/staticdocs/demo/RNAseq.r
inst/staticdocs/demo/Sardar.r
inst/staticdocs/demo/Xiang.r
inst/staticdocs/docs.r
inst/staticdocs/faq
inst/staticdocs/faq/FAQ1.r
inst/staticdocs/faq/FAQ2.r
inst/staticdocs/faq/FAQ3.r
inst/staticdocs/faq/FAQ4.r
inst/staticdocs/faq/FAQ5.r
inst/staticdocs/faq/FAQ6.r
inst/staticdocs/faq/FAQ7.r
inst/staticdocs/faq/List_faqs.txt
inst/staticdocs/images
inst/staticdocs/images/supraHex_logo.png
inst/staticdocs/images/supraHex_workflow.png
inst/staticdocs/templates
inst/staticdocs/templates/content-cite.html
inst/staticdocs/templates/content-demo.html
inst/staticdocs/templates/content-demos.html
inst/staticdocs/templates/content-docs.html
inst/staticdocs/templates/content-index.html
inst/staticdocs/templates/content-install.html
inst/staticdocs/templates/content-topic.html
inst/staticdocs/templates/footer.html
inst/staticdocs/templates/head.html
inst/staticdocs/templates/header.html
inst/staticdocs/templates/layout.html
inst/staticdocs/templates/navbar.html
man
man/Fang.Rd
man/Golub.Rd
man/Xiang.Rd
man/sBMH.Rd
man/sCompReorder.Rd
man/sDistance.Rd
man/sDmat.Rd
man/sDmatCluster.Rd
man/sDmatMinima.Rd
man/sHexDist.Rd
man/sHexGrid.Rd
man/sHexGridVariant.Rd
man/sHexPolygon.Rd
man/sInitial.Rd
man/sMapOverlay.Rd
man/sNeighAny.Rd
man/sNeighDirect.Rd
man/sPipeline.Rd
man/sTopology.Rd
man/sTrainBatch.Rd
man/sTrainSeq.Rd
man/sTrainology.Rd
man/sWriteData.Rd
man/visColoralpha.Rd
man/visColorbar.Rd
man/visColormap.Rd
man/visCompReorder.Rd
man/visDmatCluster.Rd
man/visDmatHeatmap.Rd
man/visHeatmap.Rd
man/visHeatmapAdv.Rd
man/visHexAnimate.Rd
man/visHexBarplot.Rd
man/visHexComp.Rd
man/visHexGrid.Rd
man/visHexMapping.Rd
man/visHexMulComp.Rd
man/visHexPattern.Rd
man/visKernels.Rd
man/visTreeBSclust.Rd
man/visTreeBootstrap.Rd
man/visVp.Rd
nohup.out
vignettes
vignettes/supraHex_vignettes-embryo.pdf
vignettes/supraHex_vignettes-leukemia.pdf
vignettes/supraHex_vignettes-plant.pdf
vignettes/supraHex_vignettes-sMap_bu.pdf
vignettes/supraHex_vignettes-sMap_cu.pdf
vignettes/supraHex_vignettes-sMap_ep.pdf
vignettes/supraHex_vignettes-sMap_ga.pdf
vignettes/supraHex_vignettes-sMap_gm.pdf
vignettes/supraHex_vignettes-sReorder.pdf
vignettes/supraHex_vignettes.Rnw
vignettes/supraHex_vignettes.bib
supraHex documentation built on May 21, 2017, 12:34 a.m.

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