OmniMapFree - Design - graph data

Updated: 14 July 2011.

graph data

This is used to display a graph or histogram along a chromosome, e.g. the SNP density using the count of SNPs/50,000 nt. The value of the last field on a data line is used to determine the y-value on the graph.

This is part of the data file for snps_density_graph.graph:

# clRed
# min	0	max	151
# chrom	start	end	SNPs

1	1	50000	1
1	50001	100000	0
1	100001	150000	11
1	150001	200000	41
1	200001	250000	31
1	250001	300000	36
1	300001	350000	50
1	350001	400000	50

This shows the SNP density as a graph or histogram.

The first #-line is essential and contains the colour used to draw the graph.

The second #-line is not essential but contains the max and min values used to draw the y-axis of the graph. If this is not present OmniMapFree finds these values by checking all the data.

The third line is blank and is not essential but separates the #-line from the data lines.

The following lines contain the data for each feature displayed. The first three data fields: chromosome id (chrom), start position (start) and end position (end) are used by OmniMapFree for the x-axis.

The last data field contains the value used for the y-axis.

The max value provided on the second #-line can be used to change the scale of the graph. The top of a chromosome is set to the max y-value - this makes it easier to see variations in the lower data values. Any data values greater than the "max" are reduced to the max value and are drawn as a black line to indicate that they have been truncated.

Here is the map drawn by the snps_density_graph.graph data file: