Synthesis-View

Synthesis-View is a data visualization application. Through the use of stacked data-tracks, information on SNP genomic locations, presence of the SNP in a specific study or analysis, as well as related information such as genetic effect size and summary phenotype information, are available for plotting according to user preference.

Files

Required Input File

This file is required and contains information for plotting the p values and effect size (beta) values for the SNPs in the results. The file must be a text, tab-delimited file with a header line. The order of columns does not matter in this file but the column names do. There are 3 required columns:

SNP

Chr

pos

SNPName is an optional column that specifies the name of the SNP to display on the plot. If absent, the SNP column is used.

SNPcolor is an optional column that specifies the text color for SNPs displayed. The colors can be specified in one of several formats that RMagick understands. Synthesis-View defaults to black for SNP names unless the input file specifies SNPcolor.

SNPs that do not have position information the Synthesis-View standard file are excluded from the plot.

Columns need to have a valid type specified. Valid types are pval (p value), es (effect size), betauci (effect size upper confidence interval), betalci (effect size lower confidence interval), N (sample size), caf (coded allele frequency), cases (total cases), controls (total controls), cafcases (coded allele frequency for cases), cafcontrols (coded allele frequency for controls), power and study (number of studies included).

Group membership can be specified in two ways.

1. Sample Synthesis-View Standard file
   Each SNP occupies a single line of the input file. The format is group:type. For example, a p value column for the group 'MainGroup' would have the column header MainGroup:pval. Subgroups are specified with the format group:subgroup:type. For example, if there are two groups (group1, group2) and two racial/ethnic groups within group1 and group2, the headers can be specified as:

   group1:AA:pval

   group2:AA:pval

   group1:EA:pval

   group2:EA:pval

2. Alternative Synthesis-View Standard file
   A third basic input type exists for interaction inputs. In this case the file needs SNP1 and SNP2 columns to identify the two SNPs in the plot. For this file, Chr and pos are not required as the position track will not be included in the plot.

   group	subgroup	pval
   group1	AA	0.28
   group1	EA	0.50
   group2	AA	0.77
   group2	EA	0.31

3. Interaction Synthesis-View Input file
   Alternatively, a group and a subgroup column can be used to specify that information. In this case, a SNP will be repeated for each group/subgroup in the file. For example, in the case of two groups, the file would display the information as below:

   SNP1	SNP2	group1:pval	group2:pval
   rs1020	rs1035	0.28	0.02
   rs1030	rs1026	0.50	0.55
   rs1024	rs1010	0.77	0.17

Alternatively, to create a forest plot view, the file may contain columns for odds ratio results and upper and lower confidence intervals. These should be specified as 'or', 'upper_ci' and 'lower_ci' along with the group identifier. These results than can then be plotted in conjunction with the 'Produce forest plot?' checkbox on the input form to produce a forest plot image.

Sample Synthesis-View Odds Ratio file

Phenotype Summary File

Synthesis-View accepts an optional file listing phenotypic and/or sample size summary information for the groups in the Synthesis-View input file. The required column is Group (information on what group the sample size and/or phenotype measurements correspond to).

To specify colors for the groups use the column header Color. The colors can be specified in one of several formats that RMagick understands.

Group totals and phenotype averages can be shown using the following columns: Samples (sample-size for each group), Avg Pheno (the mean of the phenotype for that respective group), and Std Dev (standard deviation of the respective phenotype).

Columns that create a box plot of the summary information are: Median (median value for each group), 25% (25th percentile), 75% (75th percentile), Min (minimum value in the group), and Max (maximum value in the group).

Group

Color

Samples

Avg Pheno

Std Dev

Sample phenotype summary file

Gene Summary File

This optional file lists information for genes represented in the results. It typically gives position information for genes. The first line contains header columns as below.

Name

Chr

Start

End

Sample Gene Summary File

LD File

The LD file is optional and follows the format of the LD file output by Haploview. (Haploview LD File)

Sample LD file

Abbreviation File

This tab-delimited file lists expanded definitions for the identifiers in the Synthesis-View Standard File.

Abbreviation

Definition

Sample Abbreviation file

SNP Source File

This tab-delimited file lists source or other tags for inclusion in an interaction plot.

SNP

Source

Sample SNP Source file

Required Options

Title

Any text can be entered and will be displayed centered across the top of the plot.

Format

Currently PheWAS-View will produce images in one of the following formats:

• PNG
• JPG

General Plot Features

Larger font

Produce a plot with larger sized text than the default.

Grayscale

When selected, only shades of gray will be used to differentiate the different groups in the plot.

Axis scaling

If set to “maximum”, axes limits will start and end utilizing the range of the data with tick-marks at regular intervals. 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

Place additional SNP locations between ends of the chromosomes on the distance track.

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.

Odds ratio and forest plot options

Produce forest plot

Produce a forest plot in Synthesis-View from odds-ratio results

Minimum forest plot x-axis at zero

Set the minimum value of the forest plot 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 odd ratio larger

Odds ratio results greater than 1.0 will be plotted as larger circles/squares.

Draw legend

Place legend for forest plot on final image

P-Value options

Include p-value track

Final image includes p-value track when checked.

Plot p-values as circles

Plots p-values as circles in place of triangles that include direction of effect.

Draw line at this p-value

Specifies a red line across the p-value track at the specific p-value of interest.

Maximum y-axis setting for p-value track

Specifies the maximum value for the p-value track in order to limit the range. Any p-value result more significant than this cutoff value will be plotted at the cutoff value in a larger size.

Highlighted group

The specified group will be plotted as diamonds instead of circles for all applicable tracks.

Other options

Include direction of effect

This option controls production of the direction of effect track.

LD D-prime track

If linkage disequilibrium information is included as an input file, select this to include a d-prime correlation track.

LD R-squared track

If linkage disequilibrium information is included as an input file, select this to include an R-squared correlation track.

SNP position track

Include location track for SNP positions.

Power track

Include power track

Interaction plot

Creates an interaction plot. Used in conjunction with a SNP source file and an input file listing SNP1 and SNP2.