Construct a plaid plot of differential interactions

Description

Plot differential interactions in a plaid format with informative coloring.

Usage

plotDI(data, fc, first.region, second.region=first.region, col.up="red", 
    col.down="blue", background="grey70", zlim=NULL, xlab=NULL, ylab=NULL, 
    diag=TRUE, ...)

rotDI(data, fc, region, col.up="red", col.down="blue", background="grey70", 
    zlim=NULL, xlab=NULL, max.height=NULL, ylab="Gap", ...)

Arguments

Details

The plotDI function constructs a plaid plot on the current graphics device. The intervals of first.region and second.region are represented by the x- and y-axes, respectively. Each bin pair is represented by a box in the plotting space, where each side of the box represents a bin. Plotting space that is not covered by any bin pair is shown in background.

The color of the box depends on the magnitude and sign of the log-fold change in fc. Positive log-FCs will range from white to col.up, whereas negative log-FCs will range from white to col.down. The chosen color is proportional to the magnitude of the log-FC, and the most extreme colors are only obtained at the maximum absolute log-FC in fc. The maximum value can be capped at zlim for better resolution of small log-FCs.

If diag=TRUE, boxes will also be plotted above the diagonal for intra-chromosomal plots. This is set as the default to avoid confusion when first.region is not set as the anchor range, i.e., it has a lower sorting order than second.region. However, this can also be turned off to reduce redundancy in visualization around the diagonal.

The rotDI function constructs a rotated plot of differential interactions, for visualization of local changes. See rotPlaid for more details.

Value

A (rotated) plaid plot of differential interactions is produced on the current graphics device. A function is also invisibly returned that converts log-FCs into colors. This is useful for coordinating the colors, e.g., when constructing a separate color bar.

Author(s)

Aaron Lun

References

Lieberman-Aiden E et al. (2009). Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326, 289-293.

See Also

plotPlaid, rotPlaid, squareCounts

Examples

# Setting up the objects.
a <- 10
b <- 20
regions <- GRanges(rep(c("chrA", "chrB"), c(a, b)), IRanges(c(1:a, 1:b), c(1:a, 1:b)),
    seqinfo=Seqinfo(seqlengths=c(chrA=a, chrB=b), seqnames=c("chrA", "chrB")))

set.seed(3423)
all.anchor1 <- sample(length(regions), 500, replace=TRUE)
all.anchor2 <- as.integer(runif(500, 1, all.anchor1+1))
out <- InteractionSet(matrix(0, 500, 1), colData=DataFrame(lib.size=1000),
        GInteractions(anchor1=all.anchor1, anchor2=all.anchor2, 
            regions=regions, mode="reverse"), metadata=List(width=1))
fc <- runif(nrow(out), -2, 2)

# Constructing intra-chromosomal DI plots around various regions
plotDI(out, fc, first.region=GRanges("chrA", IRanges(1, 10)), 
    second.region=GRanges("chrA", IRanges(1, 10)), diag=TRUE)
plotDI(out, fc, first.region=GRanges("chrA", IRanges(1, 10)), 
    second.region=GRanges("chrA", IRanges(1, 10)), diag=FALSE)

# Constructing inter-chromosomal DI plots around various regions
xxx <- plotDI(out, fc, first.region=GRanges("chrB", IRanges(1, 10)), 
    second.region=GRanges("chrA", IRanges(1, 20)), diag=TRUE)
plotDI(out, fc, first.region=GRanges("chrB", IRanges(1, 100)), 
    second.region=GRanges("chrA", IRanges(1, 200)), diag=TRUE, zlim=5)

# Making colorbars.
xxx((-10):10/10)
xxx((-20):20/20)

# Rotated.
rotDI(out, fc, region=GRanges("chrA", IRanges(1, 200)))
rotDI(out, fc, region=GRanges("chrB", IRanges(1, 200)))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(diffHic)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: InteractionSet
Loading required package: SummarizedExperiment
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/diffHic/plotDI.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotDI
> ### Title: Construct a plaid plot of differential interactions
> ### Aliases: plotDI rotDI
> ### Keywords: visualization
> 
> ### ** Examples
> 
> # Setting up the objects.
> a <- 10
> b <- 20
> regions <- GRanges(rep(c("chrA", "chrB"), c(a, b)), IRanges(c(1:a, 1:b), c(1:a, 1:b)),
+     seqinfo=Seqinfo(seqlengths=c(chrA=a, chrB=b), seqnames=c("chrA", "chrB")))
> 
> set.seed(3423)
> all.anchor1 <- sample(length(regions), 500, replace=TRUE)
> all.anchor2 <- as.integer(runif(500, 1, all.anchor1+1))
> out <- InteractionSet(matrix(0, 500, 1), colData=DataFrame(lib.size=1000),
+         GInteractions(anchor1=all.anchor1, anchor2=all.anchor2, 
+             regions=regions, mode="reverse"), metadata=List(width=1))
> fc <- runif(nrow(out), -2, 2)
> 
> # Constructing intra-chromosomal DI plots around various regions
> plotDI(out, fc, first.region=GRanges("chrA", IRanges(1, 10)), 
+     second.region=GRanges("chrA", IRanges(1, 10)), diag=TRUE)
> plotDI(out, fc, first.region=GRanges("chrA", IRanges(1, 10)), 
+     second.region=GRanges("chrA", IRanges(1, 10)), diag=FALSE)
> 
> # Constructing inter-chromosomal DI plots around various regions
> xxx <- plotDI(out, fc, first.region=GRanges("chrB", IRanges(1, 10)), 
+     second.region=GRanges("chrA", IRanges(1, 20)), diag=TRUE)
> plotDI(out, fc, first.region=GRanges("chrB", IRanges(1, 100)), 
+     second.region=GRanges("chrA", IRanges(1, 200)), diag=TRUE, zlim=5)
> 
> # Making colorbars.
> xxx((-10):10/10)
 [1] "#7F7FFF" "#8B8BFF" "#9898FF" "#A5A5FF" "#B2B2FF" "#BFBFFF" "#CBCBFF"
 [8] "#D8D8FF" "#E5E5FF" "#F2F2FF" "#FFFFFF" "#FFF2F2" "#FFE5E5" "#FFD8D8"
[15] "#FFCBCB" "#FFBFBF" "#FFB2B2" "#FFA5A5" "#FF9898" "#FF8B8B" "#FF7F7F"
> xxx((-20):20/20)
 [1] "#7F7FFF" "#8585FF" "#8B8BFF" "#9292FF" "#9898FF" "#9F9FFF" "#A5A5FF"
 [8] "#ABABFF" "#B2B2FF" "#B8B8FF" "#BFBFFF" "#C5C5FF" "#CBCBFF" "#D2D2FF"
[15] "#D8D8FF" "#DFDFFF" "#E5E5FF" "#EBEBFF" "#F2F2FF" "#F8F8FF" "#FFFFFF"
[22] "#FFF8F8" "#FFF2F2" "#FFEBEB" "#FFE5E5" "#FFDFDF" "#FFD8D8" "#FFD2D2"
[29] "#FFCBCB" "#FFC5C5" "#FFBFBF" "#FFB8B8" "#FFB2B2" "#FFABAB" "#FFA5A5"
[36] "#FF9F9F" "#FF9898" "#FF9292" "#FF8B8B" "#FF8585" "#FF7F7F"
> 
> # Rotated.
> rotDI(out, fc, region=GRanges("chrA", IRanges(1, 200)))
> rotDI(out, fc, region=GRanges("chrB", IRanges(1, 200)))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>