# Tools for visualizing genomics data

## Documentation for package ‘Sushi’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

addlegend | adds a legend to a Sushi plot
chromOffsets | defines chromosome offsets for plotting multi chromosomal plot (eg plotManhattan)
convertstrandinfo | Converts strand info to 1 / -1
labelgenome | Adds genome coordinates to the x-axis of a Sushi plot
labelplot | adds a letter and a title to a plot
maptocolors | maps numeric vector to color palette
maptolwd | maps numeric vector to line widths
opaque | makes colors transparent (or opaque)
plotBed | plots data stored in bed file format
plotBedgraph | plots data stored in bed file format
plotBedpe | plots data stored in bed file format
plotGenes | plots gene structure or transcript structures
plotHic | plots HiC interactio matrix
plotManhattan | plots a Manhattan plot
sortChrom | sort chromosome files by chom name
SushiColors | Generates a Sushi color palette
Sushi_5C.bedpe | Sushi_5C.bedpe
Sushi_ChIAPET_pol2.bedpe | Sushi_ChIAPET_pol2.bedpe
Sushi_ChIPExo_CTCF.bedgraph | Sushi_ChIPExo_CTCF.bedgraph
Sushi_ChIPSeq_CTCF.bedgraph | Sushi_ChIPSeq_CTCF.bedgraph
Sushi_ChIPSeq_pol2.bed | Sushi_ChIPSeq_pol2.bed
Sushi_ChIPSeq_pol2.bedgraph | Sushi_ChIPSeq_pol2.bedgraph
Sushi_ChIPSeq_severalfactors.bed | Sushi_ChIPSeq_severalfactors.bed
Sushi_DNaseI.bedgraph | Sushi_DNaseI.bedgraph
Sushi_genes.bed | Sushi_genes.bed
Sushi_GWAS.bed | Sushi_GWAS.bed
Sushi_hg18_genome | Sushi_hg18_genome
Sushi_HiC.matrix | Sushi_HiC.matrix
Sushi_RNASeq_K562.bedgraph | Sushi_RNASeq_K562.bedgraph
Sushi_transcripts.bed | Sushi_transcripts.bed
zoombox | Adds a zoom box to a plot
zoomsregion | Adds a zoom region to a plot