PheWAS-View

PheWAS-View creates visual summaries of the SNP, gene, phenotype, and association information resulting from PheWAS studies.

Options

Input file

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:

  • SNP (SNP or other region ID)
  • PHENOTYPE (phenotype name)
  • PVAL (p value)

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.

  • PHENOTYPE_CLASS (general class of phenotype)
  • GROUPS (study group)
  • ES (effect size)
  • LOWER_CI (lower confidence interval)
  • UPPER_CI (upper confidence interval)
  • N (number of samples)
  • GENE (gene name)

This PheWAS-View extended sample file displays a number of these columns.

Group file

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.

  • Label (value will be shown as label on final plot)
  • Color (color for the specified group). The colors can be specified in one of several formats that RMagick understands.
  • Names (matches the main input file groups column to identify the values for this label)
This PheWAS-View group file is an example.

Expected phenotypes file

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.

Correlations file

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.

Other options

Format

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

  • PNG
  • JPG

Class name

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.

Group list

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:

  • EA,AA,MA
  • EA
  • MA,EA

P value threshold

When specified, any p values worse than this value will be omitted from the final plot

Red line p value

A red line will be drawn across the p value plot at the specified value.

P value highlight threshold

Any p values worse than this threshold will be plotted in gray.

Title

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

Rotate?

The plot will be oriented so that the p value track and other tracks will be horizontal rather than vertical.

Narrow?

Decrease the distance between points to reduce overall size of plot.

Titled labels?

Labels for tracks are tilted.

Colors by group?

Data points will have colors assigned by the group file.

Show best?

The names of the best SNPs for each phenotype will be placed on the plot.

Sample size track?

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.

Remove lines?

The grid lines linking the phenotypes across tracks will no be displayed.

Show direction of effect?

Display the direction of effect as triangles on p-value track when the input file has that data in it (ES column).

Direction of effect?

Display the direction of effect track when the input file has that data in it (ES column).

Include gene name?

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.

PheWAS-View Sun Plot

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.

Options

Input

The input file matches the same format as the standard PheWAS-View plot presented above.

SNP Name or Phenotype Name

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

P value threshold

PheWAS-View will omit results that have p values worse than this value when it is set.

P value highlight threshold

PheWAS-View will highlight in red those p values that are better than this value when set.

Gene name?

Displays the gene name for a SNP when that information has been provided in the input file.

Increased font?

Increases the font size roughly 25% for better viewing in presentations.

Ancestry/ethnicity labels?

Adds the ancestry or ethnicity from the groups column to the labels on the plot.

Direction of effect?

Displays the direction of effect for the result (when provided in the input file) as a +/- on the labels.