Synthesis-View Option | Description |
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Title | Title for Synthesis-View plot |
Larger font | Produce a plot with larger sized text than the default |
Axis scaling | If set to "maximum", axes limits will start and end utilizing the range of the data with tick-marks at regular intervals in-between. If set to "cleaner" the axes will still encompass the range of the data, however the range will begin and end with a multiple of five or ten, and the plot tick-marks will also be a multiple of five or ten. |
Additional SNP locations | SNP location information in addition to chromosomal location range. |
Offset overlapping points | When points overlap, this setting will include "jitter", whereby overlapping points are offset horizontally to make them more distinguishable. |
Phenotype summary plot name | If phenotypic summary data will be incorporated into the Synthesis-View plot, the title for the phenotype summary plot should be specified here. |
Include p-value plot | Include plot of p-values |
Plot p-values as circles | To plot p-values as circles, instead of triangles that include direction of effect, even if direction of effect information is supplied in the Synthesis-View standard input file. |
Draw line at this p-value | Specification of a horizontal red line at a specific p-value of interest. |
Maximum y-axis setting for p-value track | Specify the maximum y-axis value for the p-value track in order to limit the range of the y-axis. Any p-value result more significant than this y-axis cutoff value will be plotted at the cutoff value in larger size. |
Highlighted Group | Set points as "diamond shape" for one specific group/substudy |
Produce forest plot | To produce a forest plot in Synthesis-View from odds-ratio results |
Minimum forest plot x-axis at zero | To set the minimum value of the forest plot x-axis to zero |
Plot case/control totals | The total numbers of cases/controls can be plotted either in two separate tracks ("split plot"), or in one track where the total numbers of cases/controls are indicated using open/closed circles ("combined plot"). |
Plot case/control CAF | The respective coded allele frequency (CAF) for cases/controls can be plotted either as two separate tracks ("split plot"), or in one track where cases/controls are indicated using open/closed circles ("combined plot"). |
Plot significant odds ratio larger | Plot significant odds-ratio results in larger size |
Draw legend | Draw legend for forest plot |
Include direction of effect track | Even if direction of effect information is supplied, this setting allows for inclusion/exclusion of a direction of effect track. |
Effect label | Choice of effect size label |
Linkage disequilibrium D-prime plot | If linkage disequilibrium information is included as an input file, select this to include a d-prime correlation track. |
Linkage disequilibrium R-squared plot | If linkage disequilibrium information is included as an input file, select this to include an R-squared correlation track. |
High resolution image (300 dpi) | Select to produce a 300 dpi image, otherwise the image is 72 dpi |
Image format | Choices of image format include PNG, JPEG, and TIFF |
Output file name | Choice of file name for output Synthesis-View plot |