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Table 1 Synthesis-View plotting options

From: Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis

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