1 A list of plots
1.1 JavaScript
This figure starts with a default and is updated when selected for one of the two alternatives.
htmltools::tags$iframe(src ="lz.htm", width = "100%", height = "600px")THe HTML skeleton (lz.htm) takes a file named top_hits.json containing the menu items,
[
["A1BG", "rs145685027", "19:58948122"],
["ACE", "rs4353", "17:61570422"]
]each corresponds to a file for GWAS summary statistics as shown below
> d <- jsonlite::fromJSON("vignettes/data/ACE-rs4353.json")
> class(d)
[1] "list"
> lapply(d,class)
$ppid
[1] "character"
$data
[1] "data.frame"
> lapply(d,head,3)
$ppid
[1] "ACE-rs4353"
$data
variant position ref_allele alt_allele_freq beta log_pvalue
1 17:61322094_G/T 61322094 G 0.0154 -0.1899 0.69
2 17:61322221_G/A 61322221 G 0.1905 0.0190 0.22
3 17:61322307_G/T 61322307 G 0.9682 0.4065 5.65
> j <- jsonlite::toJSON(lapply(d,head,3))
> j
{"ppid":["ACE-rs4353"],"data":[{"variant":"17:61322094_G/T","position":61322094,"ref_allele":"G","alt_allele_freq":0.0154,"beta":-0.1899,"log_pvalue":0.69},{"variant":"17:61322221_G/A","position":61322221,"ref_allele":"G","alt_allele_freq":0.1905,"beta":0.019,"log_pvalue":0.22},{"variant":"17:61322307_G/T","position":61322307,"ref_allele":"G","alt_allele_freq":0.9682,"beta":0.4065,"log_pvalue":5.65}]}1.2 Shiny
This is a skeleton for possibly interactive use.
library(shiny)
# Define a list of protein-pQTL pairs with named elements
protein_pqtl_pairs <- list(
"A1BG" = c("A1BG", "rs145685027", "19:58948122"),
"ACE" = c("ACE", "rs4353", "17:61570422")
)
# Define a list of image URLs corresponding to each protein-pQTL pair
image_urls <- c(
"https://example.com/image1.jpg",
"https://example.com/image2.jpg"
)
ui <- fluidPage(
titlePanel("Protein-pQTL"),
sidebarLayout(
sidebarPanel(
selectInput("imageSelect", "Protein-pQTL pair:",
choices = names(protein_pqtl_pairs),
selected = names(protein_pqtl_pairs)[1])
),
mainPanel(
imageOutput("selectedImage")
)
)
)
server <- function(input, output) {
output$selectedImage <- renderImage({
selected_pair <- protein_pqtl_pairs[[input$imageSelect]]
# Use the first element of the vector returned by match
selected_image_url <- image_urls[match(selected_pair, protein_pqtl_pairs)[1]]
list(src = selected_image_url, alt = "Selected Image")
}, deleteFile = FALSE)
}
shinyApp(ui, server)