From Genome Analysis Wiki
→Generate single plots using our publicly-available lipids GWAS data
| Theme || theme=”pub” || We have created a theme that has larger text and is more easily readable for publication.
| Show Annotation || showAnnot=T<br>showRefsnpAnnot=T<br>annotPch=”1,24,24,25,22,21,8,7” || SNP annotation is available for all 1000G SNPs (Aug 2009 release) and can be displayed on the plot using this option. On the website, various annotation options can be turned on or off.<br>Certain annotation fields can be turned on or off using the annotPch command. To show several categories of SNPs as the same symbol, simply give the same R symbol code for those categories (e.g. annotPch=
”1,24,24, 24, 21, 21, 21, 21”). The category listings, together with their default symbol setting are;<br>Framestop (24, triangle)<br>Splice (24, triangle)<br>NonSynonymous (25, inverted triangle)<br>Synonymous (22, square)<br>UTR (22, square)<br>TFBScons (8, star)<br>MCS44 Placental (7, square with diagonal lines)<br>None-of-the-above (21, filled circle)
| Recombination Rate Overlay || showRecomb=T || The estimated recombination rate from HapMap samples can be shown on the plot, or left off. The data plotted are from Hapmap; http://hapmap.ncbi.nlm.nih.gov/downloads/recombination/2008-03_rel22_B36/rates/