Plot scatterplot of differential expression contrast

Usage

plotContrastScatter(object, ...)

# S4 method for class '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.

Examples

data(deseq)

## DESeqAnalysis ====
plotContrastScatter(deseq, i = 1L)
#> Contrast: condition_B_vs_A
#> Factor column: condition
#> Numerator samples: "sample7", "sample8", "sample9", "sample10", "sample11"...
#> Denominator samples: "sample1", "sample2", "sample3", "sample4", "sample5"...