R Script: Creating Ideograms for S pombe Chromosomes for Use With Gviz

Purpose:
Bioconductor packages such as Gviz can plot sequencing data alongside an ideogram or karyogram representing a chromosome and which show cytobands representing Giemsa staining and the position of the centromere. The example below is taken from the Gviz User Guide, note the IdeogramTrack at the top of the image.

For many organisms this data is readily available online and Gviz will download the required files from the UCSC database to produce the IdeogramTrack.  No data is present for S. pombe, we will instead create a cytoband file for each chromosome and then create the Ideogram using the R script below.  Note that no cytoband data from Giemsa staining is available for S. pombe so our ideogram will simply represent the length of the chromosome, the position of the centromere, the teleomeres, and location of rRNA repeat sequences.
The first step is to create a cytoband file for each of the S. pombe chromosomes. The cytoband file is simply a tab delimited text file with five columns -  chrom, chromStart, chromEnd, name, gieStain.  The first four columns are self-explanatory.  The fifth column takes a value which specifies the feature to be drawn at the specified co-ordinates - recognized stain values are: gneg, gpos50, gpos75, gpos25, gpos100, acen, gvar, and stalk.

The stain values we will use are:
gneg - Negative Giesma stain - no bands drawn.
gpos25, gpos50, gpos75, gpos100 - % of Positive Giesma staining - the higher the percentage the darker the band drawn.
acen - Draws the centromere.

Text Files: All co-ordinates taken from PomBase, chromosome lengths are listed in the headers of the GFF files. We need to create three files, one for each chromosome.

cytoband_chr1.txt
chrom chromStart chromEnd name gieStain
chr1 0 29663 c212 gpos25
chr1 29663 3753687 leftArm_Chr1 gneg
chr1 3753687 3789421 centro_Chr1 acen
chr1 3789421 5554844 rightArm_Chr1 gneg
chr1 5554844 5579133 c750 gpos25

cytoband_chr2.txt
chrom chromStart chromEnd name gieStain
chr2 0 39186 c212 gpos25
chr2 29663 1602264 leftArm_Chr2 gneg
chr2 1602264 1644747 centro_Chr2 acen
chr2 1644747 4500619 rightArm_Chr2 gneg
chr2 4500619 4539804 pT2R1 gpos25

cytoband_chr3.txt
chrom chromStart chromEnd name gieStain
chr3 0 25000 rDNA_L_3 gpos50
chr3 25001 1070904 leftArm_Chr3 gneg
chr3 1070904 1137003 centro_Chr3 acen
chr3 1137003 2440000 rightArm_Chr3 gneg
chr3 2440001 2452883 rDNA_R_3 gpos50

Implementation:

library(Gviz)
#ideogram Object for Chr1
ideogramData_chr1 <- read.table(file = "/Users/Cuthbert/Desktop/cytoband_chr1.txt",
                           header = TRUE,
                           sep = "\t",
                           stringsAsFactors = FALSE)
 
itrack_chr1 <- IdeogramTrack(chromosome="chr1",
                             genome = "S.pombe",
                             name=NULL,
                             bands=ideogramData_chr1)
 
plotTracks(itrack_chr1, from=0, to=5579133)
 
#ideogram Object for Chr2
ideogramData_chr2 <- read.table(file = "/Users/Cuthbert/Desktop/cytoband_chr2.txt",
                                header = TRUE,
                                sep = "\t",
                                stringsAsFactors = FALSE)
 
itrack_chr2 <- IdeogramTrack(chromosome="chr2",
                             genome = "S.pombe",
                             name=NULL,
                             bands=ideogramData_chr2)
 
plotTracks(itrack_chr2, from=0, to=4539800)
 
#ideogram Object for Chr3
ideogramData_chr3 <- read.table(file = "/Users/Cuthbert/Desktop/cytoband_chr3.txt",
                                header = TRUE,
                                sep = "\t",
                                stringsAsFactors = FALSE)
 
itrack_chr3 <- IdeogramTrack(chromosome="chr3",
                             genome = "S.pombe",
                             name=NULL,
                             bands=ideogramData_chr3)
 
plotTracks(itrack_chr3, from=0, to=2452883)

  
#Pombe values Used:
 
# I 1 5579133  
# CEN 1:  I:3753687-3789421
# Chromosome I left c212 (coordinates 1-29663)
# Cromosome I right c750 (5554844-5579133)
# 
# II 1 4539804
# CEN 2: II:1602264-1644747
# Chromosome II left c1348 (1-39186)
# Chromosome II right pT2R1 (4500619-4539800)
# 
# III 1 2452883
# CEN 3: III:1070904-1137003
# There are no telomere proximal clones for chromosome III as the unsequenced rDNA
# blocks occur inbetween the sequenced portion and the telomeres on both chromosome arms.

The finished output for each chromosome will look similar to:

The IdeogramTracks we have created can now be passed to Gviz when plotting our data.  Another useful track which we can add to our Gviz plots is an axis showing the genomic coordinates:

# plotting axis for S. pombe with Gviz
ChrI_axis<-GenomeAxisTrack(range = IRanges(start= 3753687, end = 3789421, names = "centromere" ))
ChrII_axis<-GenomeAxisTrack(range = IRanges(start= 1602264, end = 1644747, names = "centromere" ))
ChrIII_axis<-GenomeAxisTrack(range = IRanges(start= 1070904, end = 1137003, names = "centromere" ))
plotTracks(ChrI_axis, from =1 , to= 5579133)
plotTracks(ChrII_axis, from =1 , to= 4539804)
plotTracks(ChrIII_axis, from =1 , to= 2452883)