Package index • gghic

All functions

ChromatinContacts-class: ChromatinContacts S4 class
ChromatinContacts(): Create a ChromatinContacts object
MultiWayContacts(): MultiWayContacts S4 class
as_tibble(): Convert ChromatinContacts to tibble
build(): Build hypergraph from multi-way contacts
concatemers2Gis(): Convert multi-way concatemer reads to pairwise Hi-C interactions
`features<-`(): Set genomic features in ChromatinContacts object
features(): Get genomic features
focus(): Get focus regions
geom_annotation(): Add gene annotation tracks to Hi-C plots
geom_concatemer(): Visualize multi-way contact concatemers below Hi-C map
geom_concatemer2(): Visualize concatemers (a second version)
geom_hic(): geom_hic
geom_hic_under(): Visualize inverted Hi-C heatmap below main contact map
geom_hypergraph(): Visualize Multi-way Contacts as Hypergraph
geom_ideogram(): Add chromosome ideogram annotation to Hi-C plot
geom_loop(): Visualize chromatin loops on Hi-C heatmap
geom_loop2(): Visualize chromatin loops (a second version)
geom_tad(): Visualize TAD boundaries on Hi-C heatmap
geom_tad2(): Visualize TAD boundaries (a second version)
geom_track(): Add genomic signal tracks to Hi-C plots
geom_track2(): Add genomic signal tracks with direct data input (a second version)
getBreaksLabels(): Generate axis breaks and labels for multi-chromosome plots
gghic(): Create Hi-C visualization plot
gghypergraph(): Visualize multi-way chromatin contacts as hypergraph network
hypergraphData(): Get hypergraph data from MultiWayContacts object
import(<ChromatinContacts>,<ANY>,<ANY>): Import chromatin contact data
import(<MultiWayContacts>,<ANY>,<ANY>): Import multi-way contact data
interactions(<ChromatinContacts>): Get interaction data
plotCoverageCurve(): Plot Coverage Fraction by Resolution
plotResolutionCoverage(): Plot Resolution vs Coverage
calculateResolutionDepth() calculateGenomeCoverage() findOptimalResolution() readPairsCache() calcResDepthChunked() calcGenomeCovChunked() findOptResChunked(): Calculate Resolution and Depth for Pairs Data
resolution(): Get resolution of ChromatinContacts object
scaleData(): Scale and transform Hi-C interaction data for visualization
select(): Select top hyperedges for visualization
seqinfo(<ChromatinContacts>): Get sequence information
subsetByOverlaps(<ChromatinContacts>,<numeric>) subsetByOverlaps(<ChromatinContacts>,<logical>) subsetByOverlaps(<ChromatinContacts>,<GRanges>) subsetByOverlaps(<ChromatinContacts>,<GInteractions>) `[`(<ChromatinContacts>,<numeric>,<ANY>,<ANY>) `[`(<ChromatinContacts>,<logical>,<ANY>,<ANY>) `[`(<ChromatinContacts>,<GRanges>,<ANY>,<ANY>) `[`(<ChromatinContacts>,<GInteractions>,<ANY>,<ANY>) `[`(<ChromatinContacts>,<character>,<ANY>,<ANY>): Subset ChromatinContacts objects by various criteria
theme_hic(): ggplot2 theme optimized for Hi-C contact maps
tidy(): Tidy hypergraph to long format