dash_bioManhattanPlot Examples and Reference

see ManhattanPlot in action.

ManhattanPlot

An example of a default ManhattanPlot component without any extra properties.

Threshold value 

library(dashBio)
library(data.table)

app <- Dash$new()

data = read.table("https://git.io/manhattan_data.csv",
                  header = TRUE, sep = ",")

genMark <- function(n){
    l <- list(sprintf('%s', n))
    names(l) <- 'label'
    return(l)
}

genMarks <- function(min, max, by){
    s <- seq(from=min, to=max, by)
    l <- lapply(s, genMark)
    names(l) <- s
    return(l)
}

app$layout(htmlDiv(list(
    'Threshold Value',
    dccSlider(
        id = 'default-manhattanplot-input',
        min = 1,
        max = 10,
        step = 1,
        value = 6,
        marks = genMarks(1,10,1)
    ),
    htmlBr(),
    htmlDiv(
        dccGraph(
            id = 'default-manhattanplot',
            figure = dashbioManhattan(
                dataframe = data
            )
        )
    )
)))

app$callback(
    output(id = "default-manhattanplot", property = "figure"),
    params = list(
        input(id = 'default-manhattanplot-input', property = 'value')
    ),
    update_manhattanplot <- function(threshold){
        return(
            dashbioManhattan(
                dataframe = data,
                genomewideline_value = threshold
            )
        )
    }
)

Customization

Line Colors

Change the colors of the suggestive line and the genome-wide line.

library(dashBio)

data = read.table("https://git.io/manhattan_data.csv",
                  header = TRUE, sep = ",")

dccGraph(
    figure = dashbioManhattan(
        dataframe = data,
        suggestiveline_color = "#AA00AA",
        genomewideline_color = "#AA5500"
    )
)

Highlighted Points Color

Change the color of the points that are considered significant.

library(dashBio)

data = read.table("https://git.io/manhattan_data.csv",
                  header = TRUE, sep = ",")

dccGraph(
    figure = dashbioManhattan(
        dataframe = data,
        highlight_color = "#00FFAA"
    )
)

dash_bio.ManhattanPlot is a Python-based component,
and may not be available in other languages.

Example Data