| plotVolcanoApp {bigPint} | R Documentation |
Plot interactive volcano plots.
plotVolcanoApp(
data = data,
dataMetrics = dataMetrics,
option = c("hexagon", "allPoints"),
pointColor = "orange"
)
data |
DATA FRAME | Read counts |
dataMetrics |
LIST | Differential expression metrics. This object must contain one column named "logFC" and one column named "PValue". |
option |
CHARACTER STRING ["hexagon" | "allPoints"] | The background of plot; default "hexagon" |
pointColor |
CHARACTER STRING | Color of overlaid points on scatterplot matrix; default "orange" |
A Shiny application that shows a volcano plot and allows users to overlay genes depending on two values, usually a statistical value (such as P-value) and a magnitude change value (such as log fold change). The user can download a file that contains the gene IDs that pass these thresholds.
# Example 1: Create interactive volcano plot of logged data using hexagon
# bins for the background.
data(soybean_cn_sub)
data(soybean_cn_sub_metrics)
app <- plotVolcanoApp(data = soybean_cn_sub,
dataMetrics = soybean_cn_sub_metrics)
if (interactive()) {
shiny::runApp(app)
}
# Example 2: Create interactive volcano plot of logged data using points for
# the background.
app <- plotVolcanoApp(data = soybean_cn_sub,
dataMetrics = soybean_cn_sub_metrics, option = "allPoints",
pointColor = "magenta")
if (interactive()) {
shiny::runApp(app)
}