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:
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 header specified. Valid headers 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.
- 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 |
- Alternative Synthesis-View Standard 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:
| group | subgroup | pval |
| group1 | AA | 0.28 |
| group1 | EA | 0.50 |
| group2 | AA | 0.77 |
| group2 | EA | 0.31 |
- Interaction Synthesis-View Input 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.
| 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
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.
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.
Sample Abbreviation file
SNP Source File
This tab-delimited file lists source or other tags for inclusion in an interaction plot.
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:
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.