plotVolcano: Volcano plot

In steinbaugh/DESeqAnalysis: DESeq2 Analysis Utilities

Description

Volcano plot

Usage

plotVolcano(object, ...)

## S4 method for signature 'DESeqResults'
plotVolcano(
  object,
  alphaThreshold = NULL,
  lfcThreshold = NULL,
  baseMeanThreshold = NULL,
  genes = NULL,
  gene2symbol = NULL,
  ntop = 0L,
  direction = c("both", "up", "down"),
  pointColor = c(downregulated = acidplots::lightPalette[["purple"]], upregulated =
    acidplots::lightPalette[["orange"]], nonsignificant =
    acidplots::lightPalette[["gray"]]),
  pointSize = 2L,
  pointAlpha = 0.8,
  ylim = 1e-10,
  histograms = FALSE,
  return = c("ggplot", "DataFrame")
)

## S4 method for signature 'DESeqAnalysis'
plotVolcano(object, i, ...)

Arguments

object	Object.
alphaThreshold	numeric(1) or NULL. Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.
lfcThreshold	numeric(1) or NULL. Log (base 2) fold change ratio cutoff threshold. If left NULL, will use the cutoff defined in the object.
baseMeanThreshold	numeric(1) or NULL. Base mean (i.e. average expression across all samples) threshold. If left NULL, will use the cutoff defined in the object. Applies in general to DESeq2 RNA-seq differential expression output.
genes	character. Gene identifiers.
gene2symbol	Gene2Symbol. Gene-to-symbol mappings. Must contain geneID and geneName columns. See Gene2Symbol for more information.
ntop	integer(1). Number of top features to label.
direction	character(1). Include "both", "up", or "down" directions.
pointColor	character(1). Default point color for the plot.
pointSize	numeric(1). Point size for dots in the plot. In the range of 1-3 is generally recommended.
pointAlpha	numeric(1) (0-1). Alpha transparency level.
ylim	numeric(1). Upper boundary limit for y-axis. Helps preserve dynamic range for gene sets containing highly significant P values (e.g. 1e-100).
histograms	logical(1). Show LFC and P value histograms.
return	character(1). Return type. Uses match.arg() internally and defaults to the first argument in the character vector.
i	Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL. For more information: help(topic = "Extract", package = "base")
...	Additional arguments.

Value

ggplot.

Functions

• plotVolcano,DESeqAnalysis-method: Passes to DESeqResults method, with gene2symbol argument automatically defined.

Note

Updated 2020-08-05.

Author(s)

Michael Steinbaugh, John Hutchinson, Lorena Pantano

See Also

CHBUtils::volcano_density_plot().

Examples

data(deseq)

## Get genes from DESeqDataSet.
dds <- as(deseq, "DESeqDataSet")
genes <- head(rownames(dds))
print(genes)

## DESeqAnalysis ====
plotVolcano(deseq, i = 1L)

## Customize the colors.
plotVolcano(
    object = deseq,
    i = 1L,
    pointColor = c(
        downregulated = "red",
        nonsignificant = "black",
        upregulated = "green"
    )
)

## Directional support (up or down).
plotVolcano(
    object = deseq,
    i = 1L,
    direction = "up",
    ntop = 5L
)
plotVolcano(
    object = deseq,
    i = 1L,
    direction = "down",
    ntop = 5L
)

## Label genes manually.
## Note that either gene IDs or names (symbols) are supported.
plotVolcano(deseq, i = 1L, genes = genes)

steinbaugh/DESeqAnalysis documentation built on Sept. 25, 2020, 5:21 a.m.