plot_UncalibratedMSErr: A boxplot of uncalibrated mass errors for each Raw file.

In PTXQC: Quality Report Generation for MaxQuant and mzTab Results

A boxplot of uncalibrated mass errors for each Raw file.

Description

Boxes are optionally colored to indicate that a MQ bug was detected or if PTXQC detected a too narrow search window.

Usage

plot_UncalibratedMSErr(
  data,
  MQBug_raw_files,
  stats,
  y_lim,
  extra_limit,
  title_sub
)

Arguments

data	A data.frame with columns 'fc.raw.file', 'uncalibrated.mass.error..ppm.'
MQBug_raw_files	List of Raw files with invalid calibration values
stats	A data.frame with columns 'fc.raw.file', 'sd', 'outOfCal'
y_lim	Range of y-axis
extra_limit	Position where a v-line is plotted (for visual guidance)
title_sub	Subtitle

Value

GGplot object

Examples

  n = c(150, 1000, 1000, 1000)
  data = data.frame(fc.raw.file = repEach(letters[4:1], n),
                    uncalibrated.mass.error..ppm. = c(rnorm(n[1], 13, 2.4),
                                                      rnorm(n[2], 1, 0.5),
                                                      rnorm(n[3], 3, 0.7),
                                                      rnorm(n[4], 4.5, 0.8)))
  stats = data.frame(fc.raw.file = letters[4:1],
                     sd_uncal = c(2.4, 0.5, 0.7, 0.8),
                     outOfCal = c(TRUE, FALSE, FALSE, FALSE))           
  plot_UncalibratedMSErr(data, MQBug_raw_files = letters[1],
                         stats, y_lim = c(-20,20), 15, "subtitle")

PTXQC documentation built on May 29, 2024, 9:26 a.m.