contrast.LFQ

Plots a scatter of the average LFQ values of each condition in a contrast. Dots will be colored by FoldChange and the size will correspond to the -log10(Padj).

contrast.LFQ(
  DEprot.analyses.object,
  contrast = 1,
  show.only.differential = FALSE,
  show.only.significant = FALSE,
  log2FC.positive.color = "firebrick",
  log2FC.negative.color = "steelblue4",
  log2FC.scale.min = NULL,
  log2FC.scale.max = NULL,
  identical.axes = TRUE,
  dot.labels = NULL,
  protein.names.pattern = "",
  labels.in.boxes = FALSE,
  label.font.size = 3,
  label.max.overlaps = 100,
  min.segment.length.labels = 0
)

Arguments

DEprot.analyses.object

An object of class DEprot.analyses.

contrast

Integer indicating the position of the contrast to use. Default: 1.

show.only.differential

Logical value indicating whether only up or down regulated proteins should be plotted. Default: FALSE.

show.only.significant

Logical value indicating whether only proteins with a significant p-value adjusted should be plotted. Notice that this is subordinated to `show.only.differential` (differential proteins pass the P-adj threshold by default). Default: FALSE.

log2FC.positive.color

String indicating any R-supported color for the positive foldchange values. Default: "firebrick".

log2FC.negative.color

String indicating any R-supported color for the negative foldchange values. Default: "steelblue4".

log2FC.scale.min

Numeric value indicating the minimum of the foldchange scale (lower values will be colored with the minimum of the scale). Default: NULL.

log2FC.scale.max

Numeric value indicating the maximum of the foldchange scale (lower values will be colored with the maximum of the scale). Default: NULL.

identical.axes

Logical value indicating whether the axes should be forces to be identical between x and y. 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: 3.

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 scatter plot of class ggplot2.

Examples

contrast.LFQ(DEprot.analyses.object = DEprot::test.toolbox$diff.exp.limma,
             contrast = 1)