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.
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:
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.
- 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
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
- 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
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|
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.
The LD file is optional and follows the format of the LD file output by Haploview. (Haploview LD File)
Sample LD file
This tab-delimited file lists expanded definitions for the identifiers in the Synthesis-View Standard File.
SNP Source File
This tab-delimited file lists source or other tags for inclusion in an interaction plot.
Any text can be entered and will be displayed centered across the top of the plot.
Currently PheWAS-View will produce images in one of the following formats: