shinylocuszoom

shinylocuszoom is a package based on htmlwidgets to integrate LocusZoom plots into a shiny app or Rmd notebook.

It is based on the LocusZoom.js library.

Installation

Using devtools to install the package (recommended)

devtools::install_url("https://github.com/EuracBiomedicalResearch/shinylocuszoom.git")

Or clone the repository, build the package and install it:

git clone https://github.com/EuracBiomedicalResearch/shinylocuszoom.git
R CMD build shinylocuszoom
R CMD INSTALL shinylocuszoom_<latest>.tar.gz # Change version according to the last version

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Usage

Once installed you can test if the package works correctly with the following commands within R

Load the package and get a JSON file

library(shinylocuszoom)

# Get a json file included in the package already formatted
jsonfile <- system.file("extdata/td2t_10_114550452-115067678.json", package="shinylocuszoom")
jsondata <- fromJSON(file=jsonfile)

Alternatively you can provide a data.frame formatted as specified in the R help as input of the LocusZoomWidget function.

Within Rstudio a LocusZoom plot appears in the Window panel, otherwise using standard R a new page in a web browser will pop-up with the LocusZoom plot.

LocusZoomWidget(
 jsondata[["data"]],
 chr = 10,
 bpstart = 114550452,
 bpend = 115067678,
 genome_build = "GRCh37",
 main_title = "TD2 association")

Integration with shinyapp

In the ui.R file or in the ui variable in the app.R file.

ui <- fluidPage(

# Application title
titlePanel("Locus zoom test"),

sidebarLayout(
  # Sidebar 
  sidebarPanel(

    # Chromosome selection
    selectInput(
      inputId = "chr",
      label = "Chromosome",
      choices = 1:22,
      selected = 1
    ),

    # Interval selection in BP
    numericInput(
      inputId = "bpstart",
      label = "Bp from",
      value = 0
    ),
    numericInput(
      inputId = "bpend",
      label = "Bp to",
      value = 0
     )
  ),

  mainPanel(
     # Rendering of the LocusZoom Plot
     LocusZoomWidgetOutput("locuszoom")
   )
 )
)

In the server.R file or in the server variable in the app.R file.

get_mydata <- function(chr, bpstart, bpend){
   # Write your own code to read a summary
   # statistic file and format as described
   # in the manual of the function 
   # LocusZoomWidget
}

output$locuszoom <- renderLocusZoomWidget({

  x <- get_mydata(
    chr = input$chr,
    bpstart = input$bpstart,
    bpend = input$bpend)

  # Using JSON blobs
  LocusZoomWidget(x,
                  chr = input$chr,
                  bpstart = input$bpstart,
                  bpend = input$bpend,
  )

  # Using API url
  url <- "http://myapi.com/api/v1/sumstat"
  LocusZoomWidget(url,
                  chr = input$chr,
                  bpstart = input$bpstart,
                  bpend = input$bpend,
  )
})

For further feature and how to integrate with shiny see the full example in the manual of the R function. See also

?LocusZoomWidget

Authors

Michele Filosi