Tools for visualizing genomics data


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Documentation for package ‘Sushi’ version 1.4.0

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