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Table 1 Listed are all the PheWAS-View plotting options, parameters, and flags (format: -flag name ) for creating PheWAS-View plots using phewas_view.rb

From: Visually integrating and exploring high throughput Phenome-Wide Association Study (PheWAS) results using PheWAS-View

Usage: phewas_view.rb

 

Standard PheWAS Plot

 

-v, --version

Show PheWAS-View version

-e phewas file

PheWAS-View formatted file for input

-o output name

Optional output name for the resultant plot

-t title

Main title for the plot (enclose in quotes)

-f image type

Image format for output (png default). Other options depend on ImageMagick installation.

-w, --lowres

Low resolution image (72 dpi)

-a, --rotate

Rotate final image 90 degrees

-p p-value threshold

p-value threshold, values less significant will be plotted in grey

-m, --maxp maximum p-value

Maximum p-value to plot. Values less significant than the specified cut off are not plotted

-R, --redline p-value

Draw a red line at the designated p-value

-b

Include direction of effect on plot

-A, --samp-size

Include sample size plot

-l ancestry map file

Optional ancestry map file

-c phenotype class names

Only results matching this phenotype class name are plotted

-B, --showbest

Display detailed information for best score at each phenotype

-x phenotype/SNP file

PheWAS expected SNP/phenotype file

-r ancestry

List of race/ethnicities to include (AA, EA, MA)

-s SNP ID

SNP ID to display from input file

-L phenotype list file

Optional phenotype list for inclusion

-N, --no-lines

No background lines drawn on plot

-C phenotype correlation file

Optional file with phenotype correlations

Sun Plot Settings

 

-S

Produce sun plot

-s SNP ID

SNP ID to display in center of sun plot

-P phenotype name

Phenotype to display in center of sun plot

-g gene name

Gene to display in center of sun plot

-G

Include gene name along with SNP, when SNP is selected for sun plot

-E

Include ancestry as description of result for sun plot

-m, --maxp p-value

Choose a p-value threshold, p-values less significant will not be plotted

-p p-value

For plotted results, any results more significant will be plotted in red

-b

To apply direction of effect for phenotypes in sun plot, - is negative direction, + is positive direction