PheWAS-View creates visual summaries of the SNP, gene, phenotype, and association information resulting from PheWAS studies.
PheWAS-View requires a text file as the data input for generating the image. The file must be tab-delimited and have the following header line and at least the following 3 columns:
This PheWAS-View sample file has been used to generate examples on this site. A number of optional columns can be included in the file and displayed on PheWAS-View plots depending on the options selected.
This PheWAS-View extended sample file displays a number of these columns.
This tab-delimited optional file allows the user to specify the mapping used in the input file for display as part of the plot. It consists of a header line and three columns.
This tab-delimited optional file specifies which phenotypes are expected to be associated with a SNP or region based on prior knowledge. These expected results will be shown in a different color compared to results that are not listed in the file. The file has no header line. Each line in the file should have the phenotype in the first column and then each additional column should be a SNP or region that is expected to be associated with that phenotype. This expected phenotype sample file displays these features.
PheWAS-View can display a correlation matrix below the results. The file is a tab-delimited table with the first line and first columns containing the phenotype names. Each cell in the table contains the correlation for that combination of phenotypes. This sample correlations file displays the expected format.
Currently PheWAS-View will produce images in one of the following formats:
Only those results that have the same phenotype class will be plotted if this option is used. It requires that the input file have a phenotype_class column in it.
Only the results for the specified groups will be plotted when this option is utilized. The groups should be specified as a comma-separated list. For example these would all be valid lists:
When specified, any p values worse than this value will be omitted from the final plot
A red line will be drawn across the p value plot at the specified value.
Any p values worse than this threshold will be plotted in gray.
Any text can be entered and will be displayed centered across the top of the plot.
The plot will be oriented so that the p value track and other tracks will be horizontal rather than vertical.
Decrease the distance between points to reduce overall size of plot.
Labels for tracks are tilted.
Data points will have colors assigned by the group file.
The names of the best SNPs for each phenotype will be placed on the plot.
When the input file has a sample size column (N) in it, this option will display those values in a track on the final plot.
The grid lines linking the phenotypes across tracks will no be displayed.
Display the direction of effect as triangles on p-value track when the input file has that data in it (ES column).
Display the direction of effect track when the input file has that data in it (ES column).
If the input file has a GENE column, include the gene name as part of the label on the plot. The gene name will be italicized.
The PheWAS-View Sun Plot is an alternative presentation of PheWAS results. It places either a SNP or a phenotype at the center of the plot and then displays the p values for each phenotype (when the SNP is at center) or each SNP (when the phenotype is the center). The length of the 'ray' corresponds to the -log10 of the p value.
The input file matches the same format as the standard PheWAS-View plot presented above.
One of these 2 fields must be filled to create the plot. The value must match either a SNP or a Phenotype within the input file
PheWAS-View will omit results that have p values worse than this value when it is set.
PheWAS-View will highlight in red those p values that are better than this value when set.
Displays the gene name for a SNP when that information has been provided in the input file.
Increases the font size roughly 25% for better viewing in presentations.
Adds the ancestry or ethnicity from the groups column to the labels on the plot.
Displays the direction of effect for the result (when provided in the input file) as a +/- on the labels.