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Jump to navigationJump to search→Generate single plots using our publicly-available lipids GWAS data
In addition to plotting your own results, you can plot the results of some publicly available GWAS. Currently, the only publicly available set of results that is include is our GWAS for loci determining blood lipid levels. Just like when you are plotting your own data, you can specify 1) an index SNP and a flanking region, 2) the chromosome together with start and stop positions (in basepairs), or 3) gene name and a flanking region.
In addition to plotting your own results, you can plot the results of some publicly available GWAS. Currently, the only publicly available set of results that is include is our GWAS for loci determining blood lipid levels. Just like when you are plotting your own data, you can specify 1) an index SNP and a flanking region, 2) the chromosome together with start and stop positions (in basepairs), or 3) gene name and a flanking region.
== Commonly Used LocusZoom Options ==
{| border="1" width="80%" align="center"
|- bgcolor="lightgray"
! Web Form
! "Hit Spec" File Key-Value Pair
! Description
|-
| Title on Plot
| title=”My Favorite Locus”
| Specifies large text displayed above the plot
|-
| Human Genome Build
| n/a
| Plots can be generated based on hg18 (the default) or hg17 positions
|-
| Legend Location
| legend=”left”
| This specifies the location of the legend within the plot, the default is auto. Auto tries to select a location that overlaps a minimal number of datapoints. (auto, left, right, none)
|-
| SNP Position Rug
| snpset=”HapMap” metalRug=”Rug SNPs”
| These options control display of tickmarks indicating SNP positions at the top of the plot. Setting snpset="HapMap", snpset="Illu318" or snpset="Affy500" display a fixed set of SNPs. (You can also try snpset="Affy500,Illu318,HapMap" to see all 3). The metalRug option displays a rug which only includes the SNPs that are actually plotted. To remove the rug in batch mode set snpset=NULL.
|-
| Number of Rows for Gene Names
| rfrows=4
| LocusZoom will automatically tries to determine the number of display rows to use for genes and gene names so they are not overlapping. This can make each plot prettier, but is not ideal when you want to compare many plots side by side. To ensure a fixed amount of space is used for gene names, use this option to set the maximum number of display rows. If LocusZoom runs out of plotting space and some genes are left out, a warning will be added to the plot.
|-
| Point Size
| weightCol=”SampleSize”
| This specifies that the “dot size” of each data points will reflect the square-root of the sample size. The default is to have all dot sizes equal.
|-
| LD Measure
| ldCol=”dprime” (“rsquare”)
| Colors data points according to the selected LD measure. The default is "rsquare".
|-
| Reference Population for LD
| n/a
| This option allows the user to specify which reference panel 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).
|-
| Highlight Region of Interest
| hiStart=425Mb hiEnd=425.1Mb
| A grey box can be used to highlight important regions of the genome – this can reflect where an association signal peaks or a region selected for sequencing, for example.
|-
| Theme
| theme=”publication”
| We have created a theme that has larger text and is more easily readable for publication.
|-
| Show Annotation
| showAnnot=T showRefsnpAnnot=T 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). <br>For more information about the annotation categories used, please see http://research.nhgri.nih.gov/tools/unisnp/?rm=ohelp
|-
| 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/
|}
[[Category:Software]]
[[Category:Software]]
