plotVolcano: Volcano plot

Description Usage Arguments Value Functions Note Author(s) See Also Examples

Description

Volcano plot

Usage

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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

Note

Updated 2020-08-05.

Author(s)

Michael Steinbaugh, John Hutchinson, Lorena Pantano

See Also

CHBUtils::volcano_density_plot().

Examples

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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.