plot.MA

Plots a MA plot log2(basemean) x log2(FoldChange) of differential expression results

# S3 method for class 'MA'
plot(
  DEprot.analyses.object,
  contrast = 1,
  up.color = "indianred",
  down.color = "steelblue",
  density.colors = colorRampPalette(colors = RColorBrewer::brewer.pal(9, "Blues"))(101),
  point.size = 2,
  point.alpha = 0.5,
  title = NULL,
  use.uncorrected.pvalue = FALSE,
  symmetric.y = TRUE,
  dot.labels = NULL,
  labels.in.boxes = FALSE,
  label.font.size = 2,
  label.max.overlaps = 100,
  min.segment.length.labels = 0
)

Arguments

DEprot.analyses.object

An object of class DEprot.analyses.

contrast

Number indicating the position of the contrast to use for the plotting.

up.color

String indicating the color to use for up-regulated proteins in the plots. Default: "indianred".

down.color

String indicating the color to use for up-regulated proteins in the plots. Default: "steelblue".

density.colors

List of colors, passed to scale_fill_gradientn, to use for the density gradient. Default: "colorRampPalette(colors = RColorBrewer::brewer.pal(9, "Blues"))(101)".

point.size

Numeric value indicating the size of the dots. Default: 2.

point.alpha

Numeric value between 0 and 1 to indicate the transparency (alpha) of the dots. Default: 0.5.

title

String indicating the title to use. Default: NULL (automatic title).

use.uncorrected.pvalue

Logical value indicating whether it should be used the normal p-value instead of the adjusted one (differential proteins numbers are recomputed). Default: FALSE, padj is used.

symmetric.y

Logical values indicating whether the y-axis scale should be symmetric or not. Default: TRUE.

dot.labels

String vector indicating labels to show on the plot that should correspond to prot.id column values. Default: NULL (no labels shown).

labels.in.boxes

Logical value indicating whether the labels should be visualized as boxes. Default: FALSE.

label.font.size

Numeric value indicating the size to use for the dot labels. Default: 2.

label.max.overlaps

Numeric value indicating the maximum number of overlaps allowed between labels. Default: 100.

min.segment.length.labels

Numeric value indicating the minimal length of the segments that connect the labels to the points. Default: 0 (segment always shown).

Value

A ggplot object.

Author

Sebastian Gregoricchio

Examples

plot.MA(DEprot.analyses.object = DEprot::test.toolbox$diff.exp.limma, contrast = 1) +
  ggplot2::ylab("log<sub>2</sub>(Fold Change FBS/6h.DMSO)")