plotContrastScatter: Plot scatterplot of differential expression contrast

In steinbaugh/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

Plot scatterplot of differential expression contrast

Description

Plot scatterplot of differential expression contrast

Usage

plotContrastScatter(object, ...)

## S4 method for signature 'DESeqAnalysis'
plotContrastScatter(
  object,
  i,
  direction = c("both", "up", "down"),
  alphaThreshold = NULL,
  baseMeanThreshold = NULL,
  lfcThreshold = NULL,
  pointColor = c(downregulated = AcidPlots::lightPalette[["purple"]], upregulated =
    AcidPlots::lightPalette[["orange"]], nonsignificant =
    AcidPlots::lightPalette[["gray"]]),
  pointSize = 2L,
  pointAlpha = 0.8,
  trans = c("log2", "log10", "identity"),
  limits = list(x = NULL, y = NULL),
  labels = list(title = TRUE, subtitle = NULL, x = TRUE, y = TRUE)
)

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")
direction	character(1). Include "both", "up", or "down" directions.
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.
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.
trans	character(1). Name of the axis scale transformation to apply. For more information: help(topic = "scale_x_continuous", package = "ggplot2")
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.
...	Additional arguments.

Value

ggplot.

Note

Updated 2022-04-15.

See Also

• https://doi.org/10.1084/jem.20200829

Examples

data(deseq)

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

steinbaugh/DESeqAnalysis documentation built on April 1, 2024, 8:30 a.m.