assocplot {comorbidPGS}

Multiple PGS Associations Plot

Description

assocplot() take a data frame of associations, return plot of the associations from assoc() (ggplot2 object or list of ggplot object)

Usage

assocplot(score_table = NULL, axis = "vertical", pval = FALSE)

Arguments

score_table

a dataframe with association results with at least the following columns:

• PGS: the name of the PGS

• Phenotype: the name of Phenotype

• Phenotype_type: either 'Continuous', 'Ordered Categorical', 'Categorical' or 'Cases/Controls'

• Effect: if Phenotype_type is Continuous, it represents the Beta coefficient of linear regression, OR of logistic regression otherwise

• lower_CI: lower confidence interval of the related Effect (Beta or OR)

• upper_CI: upper confidence interval of the related Effect (Beta or OR)

• P_value: associated P-value

axis

a character, 'horizontal' or "vertical" (the default) specifying the rotation of the plot

pval

a parameter specifying information on how to display P-value

• if pval is FALSE, P-value does not appear on the plot

• if pval is TRUE, P-value always appears next to the signal

• if pval is a number, P-value will appear if the P-value is inferior to this given number.

Value

return either:

• a ggplot object representing the association results.

• a list of two ggplot objects, accessible by $continuous_phenotype and $discrete_phenotype, if there are both Continuous Phenotypes and Discrete Phenotypes (i.e. "Categorical" or "Cases/Controls")