I am having some problems with the plot genes command on sushi.
My bed file looks like this:
chrom start stop gene score strand
1 20 32762385 32762699 DNMT3B . 1
2 20 32780318 32780465 DNMT3B . 1
3 20 32781353 32781414 DNMT3B . 1
4 20 32784758 32784859 DNMT3B . 1
5 20 32786502 32786627 DNMT3B . 1
6 20 32787230 32787451 DNMT3B . 1
7 20 32788854 32789012 DNMT3B . 1
8 20 32791601 32791708 DNMT3B . 1
9 20 32792626 32792770 DNMT3B . 1
10 20 32793536 32793595 DNMT3B . 1
11 20 32795409 32795534 DNMT3B . 1
12 20 32795650 32795694 DNMT3B . 1
13 20 32796790 32796869 DNMT3B . 1
14 20 32797187 32797299 DNMT3B . 1
15 20 32798460 32798643 DNMT3B . 1
16 20 32799244 32799328 DNMT3B . 1
17 20 32800153 32800298 DNMT3B . 1
18 20 32800835 32800925 DNMT3B . 1
19 20 32801278 32801426 DNMT3B . 1
20 20 32802385 32802470 DNMT3B . 1
21 20 32805338 32805407 DNMT3B . 1
22 20 32806209 32806327 DNMT3B . 1
23 20 32807762 32809356 DNMT3B . 1
24 20 32762424 32762699 DNMT3B . 1
25 20 32762596 32762699 DNMT3B . 1
26 20 32807762 32808280 DNMT3B . 1
27 20 32762642 32762699 DNMT3B . 1
28 20 32807762 32808069 DNMT3B . 1
29 20 32779852 32780145 DNMT3B . 1
And I am using the command:
plotGenes(DNMT3B.bed,chrom,chromstart,chromend,types="exon",col=SushiColors(5)labeltext=TRUE,maxrows=50,height=0.4,plotgenetype="box")
The quartz box appears but there is no data plotted.
I have also tried many variations of the command which also do not plot any data.
Any help would be much appreciated.