plotSampleDistributions: Plot distribution of intensities/ratios for each sample

In bartongroup/Proteus: Downstream analysis of the MaxQuant output

Plot distribution of intensities/ratios for each sample

Description

plotSampleDistributions makes a boxplot with intensity/ratio distribution for each sample.

Usage

plotSampleDistributions(
  pdat,
  title = "",
  method = c("violin", "dist", "box"),
  x.text.size = 7,
  n.grid.rows = 3,
  hist.bins = 100,
  x.text.angle = 90,
  vmin = as.numeric(NA),
  vmax = as.numeric(NA),
  log.scale = TRUE,
  log.base = 10,
  palette = cbPalette,
  fill = NULL,
  colour = NULL,
  hline = FALSE
)

Arguments

pdat	A proteusData object with peptide/protein intensities.
title	Title of the plot.
method	"box", "violin" or "dist"
x.text.size	Text size in value axis
n.grid.rows	Number of rows in the grid of facets
hist.bins	Number of bins in histograms
x.text.angle	Text angle in value axis
vmin	Lower bound on log value
vmax	Upper bound on log value
log.scale	Logical, to plot in logarithmic scale
log.base	Base of the logarithm which will be applied to data
palette	Palette of colours
fill	A metadata column to use for the fill of boxes
colour	A metadata column to use for the outline colour of boxes
hline	Logical, if true a horizontal line at zero is added

Value

A ggplot object.

Examples

library(proteusLabelFree)
data(proteusLabelFree)
plotSampleDistributions(prodat)
plotSampleDistributions(normalizeData(prodat))

bartongroup/Proteus documentation built on April 22, 2023, 5:33 a.m.