survey_gwas: plot sample size and other information about studies in IEU...

In vjcitn/gwaslake: Workshop for exploring MRC IEU GWAS analysis ecosystem with Bioconductor

plot sample size and other information about studies in IEU GWAS ecosystem

Description

plot sample size and other information about studies in IEU GWAS ecosystem

Usage

survey_gwas(
  phrases,
  datasource = gwaslake::gwidf_2021_01_30,
  title_pref = "IEU GWAS",
  title_text = paste(sQuote(phrases), collapse = ", "),
  xlab = "N controls",
  ylab = "N cases",
  ...
)

Arguments

phrases	character() vector to grep with ignore.case=TRUE in trait field, unique matching rows will be collected
datasource	data.frame with trait as a column, defaults to gwaslake::gwidf_2021_01_30; result of ieugwasr::gwasinfo() is intended input
title_pref	character(1) defaults to "IEU GWAS"
title_text	character(1) defaults to a paste of phrases with collapse=", "
xlab	character(1) x axis label defaults to "N controls"
ylab	character(1) x axis label defaults to "N cases"
...	passed to grep

Note

Returns ggplot, intended for ggplotly. When used with ggplotly, hover over points to get details such as exact definition of trait, study ID, PMID if available. For some phenotypes, numbers of cases or controls are unavailable. If this occurs for all studies assessing the selected phenotypes, an error is thrown.

Examples

requireNamespace("ggplot2")
sg = survey_gwas(c("asthma", "asthmatic")) + 
 ggplot2::theme(text=ggplot2::element_text(size=16))
if (interactive()) {
 requireNamespace("plotly")
 plotly::ggplotly(sg)
}

vjcitn/gwaslake documentation built on Aug. 9, 2022, 5:45 p.m.