Synthesis-View Option | Description |
---|---|

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 |