plot_accuracy: Compare coefficients of variation of quantifications between...

In mathiaskalxdorf/IceR: Requantification of label-free DDA proteomics data pre-analyzed by MaxQuant.

Compare coefficients of variation of quantifications between data sets.

Description

Compare coefficients of variation of quantifications between data sets.

Usage

plot_accuracy(
  list_of_data_lists,
  colors = c("darkgrey", "chocolate3"),
  Legendpos = "topleft",
  margins = c(2, 4, 4, 10),
  inset = c(-0.435, 0),
  Annotation_column = 1,
  plot_for = c("both", "protein", "peptide"),
  allow_missing_values = F,
  representation_of = c("total", "per group", "per intensity"),
  show_numbers = T,
  numbers_size = 1,
  round_to_k = T
)

Arguments

list_of_data_lists	List object containing lists of loaded MaxQuant or IceR data. Requires sample annotation to be added by function add_annotations().
colors	Colors for data sets to be compared. By default two colors are specified ("darkgrey","chocolate3")
Legendpos	Location of legend, By default set to "top"
margins	Margins aroung plot area. By default set to c(12,4,4,9)
inset	Inset of legend. By default set to c(-0.435,0)
Annotation_column	Which annotation column should be used to determine between which samples variability should be determined. By default set to 1.
plot_for	Specify if plots should be generated for protein-level ("protein"), peptide-level ("peptide") or both ("both"). By default set to "both".
allow_missing_values	Indicate if missing values are allowed during variability estimation. By default set to F.
representation_of	Indicate how results should be visualized. Select between "total","per group","per intensity". "total" = aggregate CVs into a single boxplot per data set. "per group" = aggregate CVs per annotation group per data set. "per intensity" = plot per data set CVs binned by protein/peptide abundance. By default set to "total".
show_numbers	Indicate if counts of available CVs per boxplot should be plotted. By default set to T.
numbers_size	Numeric value specifying plotting size of CV counts. By default set to 1.
round_to_k	Indicate if CV counts should be rounded to 1000 (K). By default set to T.

Details

Compare CVs between data sets.

Value

Comparison plots

mathiaskalxdorf/IceR documentation built on Aug. 1, 2022, 8:03 a.m.