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| Show RUG || snpset=”HapMap”<br>To display rug for SNPs in analysis file;<br>metalRug=”Rug SNPs” || Show a “rug” at the top of the plot – a series of vertical tick marks highlighting the positions of SNPs from HapMap CEU (here given as “HapMap”) or the markers shown in the plot (use metalRug)
| Show RUG || snpset=”HapMap”<br>To display rug for SNPs in analysis file;<br>metalRug=”Rug SNPs” || Show a “rug” at the top of the plot – a series of vertical tick marks highlighting the positions of SNPs from HapMap CEU (here given as “HapMap”) or the markers shown in the plot (use metalRug). Remove the rug in batch mode using snpset=NULL. Other options include "Affy500",or "Illu318", or use "Affy500,Illu318,HapMap" to see all 3.
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| Maximum Rows of Gene Names || rfrows=3 || LocusZoom will automatically determine the optimal number of rows to display genes and gene names so they are not overlapping. However, if the user wishes to keep all plots the same size, the maximum number of gene rows can be specified. Additional genes may be left off the figure to accommodate this feature so please use with caution. If genes are missing from the plot, this will be indicated on the plot.
| Maximum Rows of Gene Names || rfrows=3 || LocusZoom will automatically determine the optimal number of rows to display genes and gene names so they are not overlapping. However, if the user wishes to keep all plots the same size, the maximum number of gene rows can be specified. Additional genes may be left off the figure to accommodate this feature so please use with caution. If genes are missing from the plot, this will be indicated on the plot.
| Highlight Region of Interest || hiStart=425Mb<br>hiEnd=425.1Mb || A grey box can be used to highlight important regions of the genome – this can reflect the region of an association signal or a region being sequenced, etc.
| Highlight Region of Interest || hiStart=425Mb<br>hiEnd=425.1Mb || A grey box can be used to highlight important regions of the genome – this can reflect the region of an association signal or a region being sequenced, etc.
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| Theme || theme=”pub” || We have created a theme that has larger text and is more easily readable for publication.
| Theme || theme=”publication” || We have created a theme that has larger text and is more easily readable for publication.
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| Show Annotation || showAnnot=T<br>showRefsnpAnnot=T<br>annotPch=”21,24,24,25,22,22,8,7” || 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=”21,24,24,25,22,22,8,7”). 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)
| Show Annotation || showAnnot=T<br>showRefsnpAnnot=T<br>annotPch=”21,24,24,25,22,22,8,7” || 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=”21,24,24,25,22,22,8,7”). 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)
