#chrom chromStart chromEnd name score strand thickStart thickEnd reserved blockCount blockSizes chromStarts chr1 1000 2000 T1 1000 + 1000 2000 0 2 200,200, 0,800 chr1 1200 2400 T2 1000 - 1200 2400 0 3 500,800,300 0,600,900
Separately, we have a list of four heatmap boxes that we want to draw for each of these transcripts. For T1, the heatmap boxes cover bases 100-200 of the transcript (1100-1200 in the genome) and 700-800 (1700-1800 in the genome), each with two boxes labeled Case 1 and Case 2. For T2, the labels are the same but the bases covered are 200-300 and 900-1000.
-Before we can fill in the heatmap-specific extra fields, we need to finalize the block
-structure of each item, since the number of blocks determines the number of columns in the
-heatmap (and therefore the number of entries in _scoreArray and
-_labelArray). Creating heatmaps for
-the transcripts means changing the exon structure of each one - instead of
-representing exon boundaries, those fields will be used to describe the regions
-where we want to draw the heatmap boxes. We'll also need to add extra fields
+
Creating heatmaps for the transcripts means changing the exon structure of each one -
+instead of representing exon boundaries, those fields will be used to describe the regions
+where we want to draw the heatmap boxes. The number of blocks determines the number of columns
+in the heatmap (and therefore the number of entries in _scoreArray and
+_labelArray). We'll also need to add extra fields
with the remainder of the heatmap data, but let's start with the exons. We
immediately have a problem - in a BED file, the exons are expected to span the
length of the item. If our first line is intended to show a transcript on chr1
from base 1000 to 2000, then the first exon needs to start at 1000 and the last
exon needs to end at 2000, even though we don't have heatmap data for those
"exons". There are two ways to get around this.
Option 1 is to simply reduce the size of each transcript to match the extent of where we want to draw the heatmap. For that first line, if we only have heatmap data for bases 100-200 and 700-800 in the transcript (bases 1100-1200 and 1700-1800 in the genome), then those are the new bounds for our transcript (note that this means changing chromStart/End, thickStart/End, and the relative chromStarts values for the exons):
#chrom chromStart chromEnd name score strand thickStart thickEnd reserved blockCount blockSizes chromStarts chr1 1100 1800 T1 1000 + 1100 1800 0 2 100,100 0,600 chr1 1400 2200 T2 1000 - 1400 2200 0 2 100,100 0,700