plotVolcanoApp: Plot interactive volcano plots

In lrutter/bigPint: BIG multivariate data Plotted INTeractively

Plot interactive volcano plots

Description

Plot interactive volcano plots.

Usage

plotVolcanoApp(
  data = data,
  dataMetrics = dataMetrics,
  dataSE = NULL,
  option = c("hexagon", "allPoints"),
  pointColor = "orange"
)

Arguments

data	DATA FRAME | Read counts
dataMetrics	LIST | Differential expression metrics. This object must contain one column named "logFC" and one column named "PValue".
dataSE	SUMMARIZEDEXPERIMENT | Summarized experiment format that can be used in lieu of data; default NULL
option	CHARACTER STRING ["hexagon" | "allPoints"] | The background of plot; default "hexagon"
pointColor	CHARACTER STRING | Color of overlaid points on scatterplot matrix; default "orange"

Value

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.

Examples

# The first pair of examples use data and dataMetrics objects as input.
# The last pair of examples create the same plots now using the 
# SummarizedExperiment (i.e. dataSE) object input.

# 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)
}

# Below is the same pair of examples, only now using the
# SummarizedExperiment (i.e. dataSE) object as input.

# Example 1: Create interactive volcano plot of logged data using hexagon
# bins for the background.

## Not run: 
data(se_soybean_cn_sub)
app <- plotVolcanoApp(dataSE = se_soybean_cn_sub)
if (interactive()) {
    shiny::runApp(app)
}

## End(Not run)

# Example 2: Create interactive volcano plot of logged data using points for 
# the background.

## Not run: 
app <- plotVolcanoApp(dataSE = se_soybean_cn_sub, option = "allPoints",
    pointColor = "magenta")
if (interactive()) {
    shiny::runApp(app)
}

## End(Not run)

lrutter/bigPint documentation built on Nov. 11, 2023, 1 a.m.