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,
  protein.names.pattern = "",
  labels.in.boxes = FALSE,
  label.font.size = 2,
  label.max.overlaps = 100,
  min.segment.length.labels = 0,
  label.top.n = NULL
)

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).

protein.names.pattern

Character indicating a regular expression to remove from the protein IDs. Default: "", no alterations in the protein IDs.

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).

label.top.n

Single integer value (or NULL) indicating the number of top differentially expressed proteins to label automatically. Differential proteins (up- or down-regulated) are ranked by -log10(padj) * abs(log2FC) and the top N are labeled; if fewer than N differential proteins are available, all of them are labeled. When use.uncorrected.pvalue = TRUE, the uncorrected p-value is used in the ranking instead of the adjusted one. Any IDs provided through dot.labels are added to the automatically selected ones, and labels.in.boxes together with the other label aesthetics apply to them as well. Default: NULL (no automatic labels).

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)")
#> Warning: Removed 400 rows containing missing values or values outside the scale range
#> (`geom_raster()`).


plot.MA(DEprot.analyses.object = DEprot::test.toolbox$diff.exp.limma,
        contrast = 1,
        label.top.n = 10) +
  ggplot2::ylab("log<sub>2</sub>(Fold Change FBS/6h.DMSO)")
#> Warning: Removed 400 rows containing missing values or values outside the scale range
#> (`geom_raster()`).