plotMa: MA plot

In acidgenomics/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

MA plot

Description

The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales.

Usage

plotMa(object, ...)

## S4 method for signature 'DESeqAnalysis'
plotMa(
  object,
  i,
  alphaThreshold = NULL,
  baseMeanThreshold = NULL,
  lfcThreshold = NULL,
  genes = NULL,
  ntop = 0L,
  ...
)

## S4 method for signature 'DESeqResults'
plotMa(
  object,
  direction = c("both", "up", "down"),
  alphaThreshold = NULL,
  baseMeanThreshold = NULL,
  lfcThreshold = NULL,
  genes = NULL,
  ntop = 0L,
  pointColor = c(downregulated = AcidPlots::lightPalette[["purple"]], upregulated =
    AcidPlots::lightPalette[["orange"]], nonsignificant =
    AcidPlots::lightPalette[["gray"]]),
  pointSize = 2L,
  pointAlpha = 0.8,
  limits = list(x = NULL, y = NULL),
  labels = list(title = TRUE, subtitle = NULL)
)

Arguments

object	Object.
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")
alphaThreshold	numeric(1) or NULL. Adjusted P value ("alpha") cutoff. 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.
lfcThreshold	numeric(1) or NULL. Log (base 2) fold change ratio cutoff threshold. If left NULL, will use the cutoff defined in the object.
genes	character. Gene identifiers.
ntop	integer(1). Number of top features to label.
...	Additional arguments.
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.
limits	list(2). Named list containing "x" and "y" that define the lower and upper limits for each axis. Set automatically by default when left NULL.
labels	list. ggplot2 labels. See ggplot2::labs() for details.

Details

An MA plot is an application of a Bland–Altman plot for visual representation of genomic data. The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales, then plotting these values.

Value

ggplot.

Functions

• plotMa(DESeqAnalysis): Passes to DESeqResults method, with gene2symbol argument automatically defined.

Note

Updated 2022-03-08.

Author(s)

Michael Steinbaugh, Rory Kirchner

See Also

DESeq2::plotMA().

Examples

data(deseq)

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

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

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

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

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

acidgenomics/DESeqAnalysis documentation built on March 27, 2024, 10:32 p.m.