In this tutorial I describe how to represent IRanges object using different colors. For example, you may want to show the exons of a given gene with color1, and on top of the exons the forward and reverse primer sequences designed to amplify a specific amplicon with color2.

In this this tutorial I use gene and primer sequences, which are described in our 2017 PLOS ONE paper:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0172674

Set the working directory

if(!file.exists("./data")){dir.create("./data")}
setwd("./data")

Dependencies

library(IRanges)

Load functions

You can find the original funcion plotRanges under the Genomics Class repo: https://github.com/genomicsclass/ph525x/blob/master/R/plotRanges.R

Example 1

IRanges object contains both, gene and primer coordinates.
We work with the Bos taurus peptidylprolyl isomerase B (*PPIB). It is a 5 exons gene on chromosome 10. We can get the coordinates from the accession site at NCBI:
https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=281419

We can create an IRanges object with those coordinates and the postion of primer to meassure the gene expression level by qPCR.

PPIB <- IRanges(start=c(15,808,1571,4643,5574, 4806, 5617),
                end=c(125,921,1664,4827,5696, 4825, 5636), 
                names=c("exon1", "exon2", "exon3", "exon4", "exon5",
                        "Forward", "Reverse"))
PPIB
## IRanges object with 7 ranges and 0 metadata columns:
##               start       end     width
##           <integer> <integer> <integer>
##     exon1        15       125       111
##     exon2       808       921       114
##     exon3      1571      1664        94
##     exon4      4643      4827       185
##     exon5      5574      5696       123
##   Forward      4806      4825        20
##   Reverse      5617      5636        20

Plot the IRanges object using the plotRanges function.

Our goal is to color the primer sequences.
We create a vector that indexes the IRanges object containing the primer.
In this example, the primer is named as “Forward” and “Reverse”. The indexes are
captured by the function color_ind.

target <- c("Forward", "Reverse")

color_ind <- function(ir, target) {
  val <- which(names(ir) %in% target)
  val
}

color_ind(PPIB, target)
## [1] 6 7

Next, we define a new function that reads the IRanges object and the color_ind output. This function returns a vector with the colors to be used by the plotting function.

getColor <- function(ir, ind, color1, color2) {
  
  color_output <- vector("double", length(ir))
  
  for(i in seq(length(ir))) {
    if(i %in% ind) {
      color_output[i] = color2}
    else {color_output[i] = color1}
  }
  color_output
  
}

# Call the function. 
# In the example, the exons will be shown in color1, while the primer will be represented 
# using color2.
c_ind <- color_ind(PPIB, target)
color = getColor(PPIB, c_ind, 1, 2)

Finally, we modify the plotRanges function to color the selected ranges.

plotRangesColor <- function(x, xlim = x, main = deparse(substitute(x)),
                       col = color, ## modified
                       sep = 0.5, ...)
{
  height <- 1
  if (is(xlim, "Ranges"))
    xlim <- c(min(start(xlim)), max(end(xlim)))
  bins <- disjointBins(IRanges(start(x), end(x) + 1))
  plot.new()
  plot.window(xlim, c(0, max(bins)*(height + sep)))
  ybottom <- bins * (sep + height) - height
  rect(start(x)-0.5, ybottom, end(x)+0.5, ybottom + height, col = col, 
       border = col, ...)   ## modified
  title(main)
  axis(1)
  par(las = 1)
}

Call the plotRangesColor.

plotRangesColor(PPIB, col = color, xlim=c(0,5906), main="PPIB")

Example 2

Gene and primer coordinates contained in two different IRanges objects.

This example use the mRNA of the dysbindin domain containing gene (DBNDD2). It contains 3 exons and spans 1173 bp. You can take a look at the accession at NCBI:
https://www.ncbi.nlm.nih.gov/nuccore/195539544/

DBNDD2 <- IRanges(start=c(1889,2217,3680), 
                  end=c(2026,2354,3888), 
                  names = c(paste(rep("exon"),1:3, sep="")))

primer.DBNDD2 = IRanges(start=c(2270,2324), end=c(2289,2343),
                        names = c("Forward", "Reverse"))

Now we have two IRAnges objects

DBNDD2
## IRanges object with 3 ranges and 0 metadata columns:
##             start       end     width
##         <integer> <integer> <integer>
##   exon1      1889      2026       138
##   exon2      2217      2354       138
##   exon3      3680      3888       209
primer.DBNDD2
## IRanges object with 2 ranges and 0 metadata columns:
##               start       end     width
##           <integer> <integer> <integer>
##   Forward      2270      2289        20
##   Reverse      2324      2343        20

In this example, we have to create a sorted IRanges combaining both objects. Then, the rest of the procedure is similar as Example1.

sort_ir <- sort(c(DBNDD2, primer.DBNDD2))
sort_ir
## IRanges object with 5 ranges and 0 metadata columns:
##               start       end     width
##           <integer> <integer> <integer>
##     exon1      1889      2026       138
##     exon2      2217      2354       138
##   Forward      2270      2289        20
##   Reverse      2324      2343        20
##     exon3      3680      3888       209

Indexes for the ranges to color

c_ind <- color_ind(sort_ir, names(primer.DBNDD2))
c_ind
## [1] 3 4

Assign color2 to those indexes

color = getColor(sort_ir, c_ind, 1, 2)

Plot the IRAnges

plotRangesColor(sort_ir, col = color, xlim=c(1500,4100), main="DBNDD2 (AC_000170)")

The code for this tutorial is available from my Github repository:
https://github.com/jdieramon/my-scripts/blob/master/plotRangeColors.R