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Jump to navigationJump to search→Generate single plots using our publicly-available lipids GWAS data
| Human Genome Build || n/a (must be selected from web form) || Plots can be generated based on hg 18 (default) or hg17 positions
| Human Genome Build || n/a (must be selected from web form) || Plots can be generated based on hg 18 (default) or hg17 positions
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| Legend Location legend=”right” This specifies the location of the legend within the plot, the default is left
| Legend Location || legend=”right” || This specifies the location of the legend within the plot, the default is left
(left, right, none)
(left, right, none)
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| Show RUG snpset=”HapMap”
| 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)
To display rug for SNPs in analysis file;
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)
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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.
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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.
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| HapMap Population for LD || n/a (must be selected from web form) || This option allows the user to specify which HapMap population was used to obtain LD estimates. The default is CEU but users may select YRI or JPT+CHB
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| 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.
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| Format of Output File || format=”pdf,png”<br>format=”pdf”<br>format=”png” || Pdf or png output is available. The default is pdf
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| 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>Coding (22, square)<br>UTR (21, filled circle)<br>TFBScons (8, star)<br>MCS44 Placental (7, square with diagonal lines)<br>None-of-the-above (1, open circle)
| 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>Coding (22, square)<br>UTR (21, filled circle)<br>TFBScons (8, star)<br>MCS44 Placental (7, square with diagonal lines)<br>None-of-the-above (1, open circle)
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