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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). Remove the rug in batch mode using snpset=NULL. Other options include "Affy500",or "Illu318", or use "Affy500,Illu318,HapMap" to see all 3.
| 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=4 || 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.
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| Point Size Proportional to Sample Size || weightCol=”SampleSize” || This specifies that the “dot size” of the data points will reflect the square-root of the sample size (to reflect the s.e.). The default is to have all dot sizes remain the same size.
| Point Size Proportional to Sample Size || weightCol=”SampleSize” || This specifies that the “dot size” of the data points will reflect the square-root of the sample size (to reflect the s.e.). The default is to have all dot sizes remain the same size.
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| LD Measure || ldCol=”dprime” (“rsquare”) || The color of the data points reflects the LD (r2) with the index SNP.
| LD Measure || ldCol=”dprime” (“rsquare”) || The color of the data points reflects the LD (r2) with the index SNP. The default is "rsquare".
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| HapMap Population for LD || n/a (must be selected from web form) || This option allows the user to specify which population is used to obtain LD estimates. The default is CEU from HapMap Phase II but users may select YRI or JPT+CHB from HapMap Phase II, or CEU from 1000 Genomes (August 2009 release).
| HapMap Population for LD || n/a (must be selected from web form) || This option allows the user to specify which population is used to obtain LD estimates. The default is CEU from HapMap Phase II but users may select YRI or JPT+CHB from HapMap Phase II, or CEU from 1000 Genomes (August 2009 release).
