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# Upload your own meta-analysis file and generate many plots at once by uploading a specification file. Results will be emailed back to the user.
# Upload your own meta-analysis file and generate many plots at once by uploading a specification file. Results will be emailed back to the user.
== Generate single plots using our publicly-available lipids GWAS data ==
# Selecting regions to display using our lipids data
The plots were designed to examine ~ 1 Megabase windows of the genome, although for regions with several association signals or long-range linkage disequilibrium patterns, plots extending as large as a few Mb can be drawn. The user can specify the region to display in the LocusZoom plot in one of three ways; 1) an index SNP and a flanking region, 2) the chromosome together with start and stop positions (in basepairs), 3) gene name and a flanking region.
The plots were designed to examine ~ 1 Megabase windows of the genome, although for regions with several association signals or long-range linkage disequilibrium patterns, plots extending as large as a few Mb can be drawn. The user can specify the region to display in the LocusZoom plot in one of three ways; 1) an index SNP and a flanking region, 2) the chromosome together with start and stop positions (in basepairs), 3) gene name and a flanking region.
# Displaying LD information
In the main plot window, data points are colored according to their level of linkage disequilibrium (LD) with the index SNP. If users specify the region to display using an index SNP and flanking region, LD of all data points will be relative to the user-specified index SNP. If users specify the region to display using options 2 and 3 above, LocusZoom will select the most significant SNP in the region. For all other SNPs in the plot, the color of the data point will reflect the pair-wise LD patterns with this index SNP. The default LD which will be displayed is r2 from the HapMap CEU population (release 22), but users have the option to select either r2 or D’ from; HapMap CEU, HapMap YRI, Hapmap CHB+JPT, 1000 Genomes CEU. Because we have pre-computed LD for all SNPs in HapMap CEU, plots will generate very quickly if using the default LD information, provided the region to display is less than 500kb either side of the index SNP. SNPs with missing LD information are shown in grey.
In the main plot window, data points are colored according to their level of linkage disequilibrium (LD) with the index SNP. If users specify the region to display using an index SNP and flanking region, LD of all data points will be relative to the user-specified index SNP. If users specify the region to display using options 2 and 3 above, LocusZoom will select the most significant SNP in the region. For all other SNPs in the plot, the color of the data point will reflect the pair-wise LD patterns with this index SNP. The default LD which will be displayed is r2 from the HapMap CEU population (release 22), but users have the option to select either r2 or D’ from; HapMap CEU, HapMap YRI, Hapmap CHB+JPT, 1000 Genomes CEU. Because we have pre-computed LD for all SNPs in HapMap CEU, plots will generate very quickly if using the default LD information, provided the region to display is less than 500kb either side of the index SNP. SNPs with missing LD information are shown in grey.
Table 1.3 Additional options available from the web form
Table 1.3 Additional options available from the web form
Additional options that can be used when generating any type of plot
Additional options that can be used when generating any type of plot
Option when using web Option to include in specification file when using batch mode Description
{| border="1"
Title on Plot title=”My Favorite Locus” The title above the plot can be specified
|-
Human Genome Build n/a (must be selected from web form) Plots can be generated based on hg 18 (default) or hg17 positions
| Option when using web || Option to include in specification file when using batch mode || Description
|-
| Title on Plot || title=”My Favorite Locus” || The title above the plot can be specified
|-
|Human Genome Build || n/a (must be selected from web form) || Plots can be generated based on hg 18 (default) or hg17 positions
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)
Show RUG snpset=”HapMap”
Show RUG snpset=”HapMap”
|-
|}
To display rug for SNPs in analysis file;
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)
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)
