plot GInteractions

plot graph for GInteractions

loopBouquetPlot(
  gi,
  range,
  feature.gr,
  genomicSigs,
  signalTransformFun = function(x) {
     log2(x + 1)
 },
  label_region = FALSE,
  show_edges = TRUE,
  show_cluster = TRUE,
  lwd.backbone = 2,
  col.backbone = "gray",
  lwd.maxGenomicSigs = 8,
  reverseGenomicSigs = TRUE,
  col.backbone_background = "gray70",
  alpha.backbone_background = 0.5,
  lwd.gene = 2,
  lwd.nodeCircle = 1,
  col.nodeCircle = "#DDDDDD25",
  lwd.edge = 2,
  col.edge = "gray80",
  coor_mark_interval = 1e+05,
  col.coor = "black",
  show_coor = TRUE,
  coor_tick_unit = 1000,
  label_gene = TRUE,
  col.tension_line = "black",
  lwd.tension_line = 1,
  length.arrow = NULL,
  safe_text_force = 3,
  method = 1,
  doReduce = FALSE,
  ...
)

Arguments

gi

An object of GInteractions

range

The region to plot. an object of GRanges

feature.gr

The annotation features to be added. An object of GRanges.

genomicSigs

The genomic signals. An object of GRanges with scores or an object of track.

signalTransformFun

The transformation function for genomic signals.

label_region

Label the region node or not.

show_edges

Plot the interaction edges or not.

show_cluster

Plot the cluster background or not.

lwd.backbone, lwd.gene, lwd.nodeCircle, lwd.edge, lwd.tension_line, lwd.maxGenomicSigs

Line width for the linker, gene, interaction node circle, the dashed line of interaction edges, the tension line and the maximal reversed genomic signal.

col.backbone, col.backbone_background, col.nodeCircle, col.edge, col.tension_line, col.coor

Color for the DNA chain, the compact DNA chain, the node circle, the linker, the tension line and the coordinates marker.

reverseGenomicSigs

Plot the Genomic signals in reverse values.

alpha.backbone_background

Alpha channel for transparency of backbone background.

coor_mark_interval

The coordinates marker interval. Numeric(1). Set to 0 to turn it off. The default value 1e5 means show coordinates every 0.1M bp.

show_coor

Show coordinates or not.

coor_tick_unit

The bps for every ticks. Default is 1K.

label_gene

Show gene symbol or not.

length.arrow

Length of the edges of the arrow head (in inches).

safe_text_force

The loops to avoid the text overlapping.

method

Plot method. Could be 1 or 2.

doReduce

Reduce the GInteractions or not.

...

Parameter will be passed to layout_with_fr.

Value

A invisible list with the key points of the plot.

Examples

library(InteractionSet)
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: 'MatrixGenerics'
#> The following objects are masked from 'package:matrixStats':
#> 
#>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: 'Biobase'
#> The following object is masked from 'package:MatrixGenerics':
#> 
#>     rowMedians
#> The following objects are masked from 'package:matrixStats':
#> 
#>     anyMissing, rowMedians
gi <- readRDS(system.file("extdata", "gi.rds", package = "trackViewer"))
range <- GRanges("chr2", IRanges(234500000, 235000000))
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
#> Loading required package: GenomicFeatures
#> Loading required package: AnnotationDbi
library(org.Hs.eg.db)
#> 
feature.gr <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
#>   403 genes were dropped because they have exons located on both strands of the
#>   same reference sequence or on more than one reference sequence, so cannot be
#>   represented by a single genomic range.
#>   Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
#>   object, or use suppressMessages() to suppress this message.
feature.gr <- subsetByOverlaps(feature.gr, range(regions(gi)))
symbols <- mget(feature.gr$gene_id, org.Hs.egSYMBOL, ifnotfound = NA)
feature.gr$label[lengths(symbols) == 1] <- unlist(symbols[lengths(symbols) == 1])
feature.gr$col <- sample(1:7, length(feature.gr), replace = TRUE)
feature.gr$type <- sample(c("cRE", "gene"),
  length(feature.gr),
  replace = TRUE,
  prob = c(0.1, 0.9)
)
feature.gr$pch <- rep(NA, length(feature.gr))
feature.gr$pch[feature.gr$type == "cRE"] <- 11
loopBouquetPlot(gi, range, feature.gr)